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Is your feature request related to a problem? Please describe.
Running snappy-snake on large workflows is hard. Snakemake offers --batch for this.
Describe the solution you'd like
Pass this through from snappy-snake to snakemake.
Also, adjust the pipeline_job.sh template such that it can be submitted easily with sbatch --array=START-STOP. This should lead to adding --batch default=$SLURM_ARRAY_TASK_ID/$SLURM_ARRAY_TASK_MAX to the script and terminate the script if $SLURM_ARRAY_TASK_ID < 1. This will allow submitting with sbatch --array 1-10 pipeline.sh` and work through the large workflow in 10 batches.
Describe alternatives you've considered
N/A
Additional context
N/A
The text was updated successfully, but these errors were encountered:
Is your feature request related to a problem? Please describe.
Running
snappy-snake
on large workflows is hard. Snakemake offers--batch
for this.Describe the solution you'd like
Pass this through from
snappy-snake
tosnakemake
.Also, adjust the
pipeline_job.sh
template such that it can be submitted easily withsbatch --array=START-STOP
. This should lead to adding--batch default=$SLURM_ARRAY_TASK_ID/$SLURM_ARRAY_TASK_MAX
to the script and terminate the script if$SLURM_ARRAY_TASK_ID < 1. This will allow submitting with
sbatch --array 1-10 pipeline.sh` and work through the large workflow in 10 batches.Describe alternatives you've considered
N/A
Additional context
N/A
The text was updated successfully, but these errors were encountered: