How to run:

1. conda env create -f environment.yml
2. modify config.yaml if needed.
3. create folders /scratch/rchoudhu/training/slurm_out/ and /scratch/rchoudhu/training/tmp/
4. Activate gatk4 conda activate gatk4
5. snakemake -s SnakeDeepVariant -n -p
6. Create reference index in /home/rchoudhu/Resources/genome folder: gatk --java-options '-Xmx8g -Xms8g' CreateSequenceDictionary -R ref.fasta -O ref.dict samtools faidx ref.fasta bwa index -a bwtsw ref.fasta

To run on Slurm HPC:

nohup snakemake -s SnakeDeepVariant -p --cluster-config slurm_hpc.json --cluster "sbatch -J {cluster.name} -t {cluster.time} -c {cluster.cpu} --mem={cluster.mem} -p {cluster.partition} -o {cluster.output} -e {cluster.error}" --jobs 100 --latency-wait 5 &

To submit everything in one go: snakemake -s SnakeDeepVariant -p -j 9999 --immediate-submit --notemp --cluster-config slurm_hpc.json --cluster "./parseJobID.py {dependencies}" --latency-wait 120

Clean everything:

snakemake clean