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Commit ee28a73e authored by Manavalan Gajapathy's avatar Manavalan Gajapathy
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adds cli option to choose slurm partition

parent 67b7f139
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1 merge request!2QC under one umbrella (well mostly) under QuaC
......@@ -184,6 +184,7 @@ python src/run_quac.py \
# for a WGS project, and write results to a dir of choice
python src/run_quac.py \
--slurm_partition medium \
--project_name CF_CFF_PFarrell \
--pedigree data/raw/ped/CF_CFF_PFarrell.ped \
--outdir /some/lake/with/plenty/ducks/
......
......@@ -171,10 +171,17 @@ def main(args):
)
# submit snakemake command as a slurm job
slurm_partition_times = {
"express": "02:00:00",
"short": "12:00:00",
"medium": "50:00:00",
"long": "150:00:00",
}
slurm_resources = {
"partition": "medium", # express(max 2 hrs), short(max 12 hrs), medium(max 50 hrs), long(max 150 hrs)
"partition": args.slurm_partition, # express(max 2 hrs), short(max 12 hrs), medium(max 50 hrs), long(max 150 hrs)
"ntasks": "1",
"time": "12:00:00",
"time": slurm_partition_times[args.slurm_partition],
"cpus-per-task": "1",
"mem": "8G",
}
......@@ -298,6 +305,16 @@ if __name__ == "__main__":
metavar="",
)
WRAPPER.add_argument(
"--slurm_partition",
help="Request a specific partition for the slurm resource allocation for QuaC workflow. "
"Available partitions in Cheaha are: express(max 2 hrs), short(max 12 hrs), "
"medium(max 50 hrs), long(max 150 hrs)",
default="short",
choices=["express", "short", "medium", "long"],
metavar="",
)
ARGS = PARSER.parse_args()
main(ARGS)
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