Pass a script to sbatch rather than --wrap to avoid hitting SLURM command-line character limit #379
Description
Is your feature request related to a problem? Please describe.
On some clusters, there are strict limits to SLURM command-line length and the "wrapped" command sent to sbatch might trigger the limit in case of many input files or multiple item group-components.
The following error then happens :
sbatch: error: Batch job submission failed: Pathname of a file, directory or other parameter too long
Describe the solution you'd like
When submitting the SLURM job, instead of using sbatch --wrap, use sbatch script.sh and put the contents of "wrap" (the command to send to sbatch) into script.sh
Describe alternatives you've considered
N/A
Additional context
Same should also be done in snakemake-executor-plugin-slurm-jobstep
Relevant commits:
dmwnz@212c274
dmwnz/snakemake-executor-plugin-slurm-jobstep@2f9d19b