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fix: allow to pass single batch number to pipeline_job.sh (#327) #333

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merged 1 commit into from
Jan 10, 2023
Merged

fix: allow to pass single batch number to pipeline_job.sh (#327) #333

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13 changes: 3 additions & 10 deletions snappy_pipeline/apps/tpls/pipeline_job.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -111,19 +111,12 @@ set -x
# Kick off Snakemake --------------------------------------------------------

# Interpret array jobs.
set +e
SNAKEMAKE_BATCH_END=${SLURM_ARRAY_TASK_MAX-}
SNAKEMAKE_BATCH_CUR=${SLURM_ARRAY_TASK_ID-}
if [[ ! -z "$SNAKEMAKE_BATCH_CUR" ]]; then
if [[ $SLURM_ARRAY_TASK_ID -lt 1 ]]; then
>&2 echo "Snakemake batches start couting at 1"
exit 1
fi
SNAKEMAKE_BATCH_ARG="--batch ${SNAKEMAKE_BATCH_RULE-default}=${SNAKEMAKE_BATCH_CUR}/${SNAKEMAKE_BATCH_END}"
# Allow selection of batch
if [[ ! -z "${SNAPPY_BATCH-}" ]]; then
SNAKEMAKE_BATCH_ARG="--batch ${SNAKEMAKE_BATCH_RULE-default}=${SNAPPY_BATCH}"
else
SNAKEMAKE_BATCH_ARG=
fi
set -e

# Using the medium project/queue is a sensible default.
snappy-snake --printshellcmds \
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