uab-cgds-worthey / quac

🦆 Quality Control of WGS and exome samples 🦆
https://quac.readthedocs.io
GNU General Public License v3.0
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CLI script not accounting for user's environment specific slurm args requirements #76

Closed ManavalanG closed 1 year ago

ManavalanG commented 1 year ago

A reviewer ran into error due to slurm related issues when slurmpy attempts to submit the parent quac job to slurm.

We believe we fixed a variation of this issue in #73 where snakemake would be submitting jobs to slurm. Ideally we should have fixed above issues as part of that PR, but we didn't catch it back then.

Planned solution:

    slurm_resources = {
        "partition": args.slurm_partition,
        "ntasks": "1",
        "time": slurm_partition_times[args.slurm_partition],
        "cpus-per-task": "1" if args.subtasks_slurm else "4",
        "mem-per-cpu": "8G",
    }

add a step to read cluster config file and include any args that are not already in slurm_resources

ManavalanG commented 1 year ago

Quick note - solution we ended up using was to provide slurm info as a input config file.