Run the workflow using toil-cwl-runner on the ARA Slurm cluster with Singularity - Githubissues

zmahnoor14 / MAW

Metabolome Annotation Workflow

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Run the workflow using toil-cwl-runner on the ARA Slurm cluster with Singularity #26

Open mr-c opened 1 year ago

mr-c commented 1 year ago

[ ] Add [ResourceRequirements] (https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement) with ramMin and coresMin for all the CommandLineTools

# in a Python 3.7 environment (or newer)
# also nice if nodejs is available (this is not required for MAW as of 2022-12-16)
pip install toil[cwl]
export TOIL_SLURM_ARGS="--partition=thin" # set queue name and any other required arguments for sbatch (but not memory or cores
toil-cwl-runner --singularity --batchSystem slurm --disableCaching true --outdir results_1 maw.cwl maw_job.yaml

(alas, toil-cwl-runner does not support --provenance yet)