diff --git a/sequence_processing_pipeline/templates/nuqc_job.sh b/sequence_processing_pipeline/templates/nuqc_job.sh index 3561f67c..9451956f 100644 --- a/sequence_processing_pipeline/templates/nuqc_job.sh +++ b/sequence_processing_pipeline/templates/nuqc_job.sh @@ -12,18 +12,13 @@ echo "---------------" echo "Run details:" -echo "$SLURM_JOB_NAME $SLURM_JOB_ID $SLURMD_NODENAME" +echo "$SLURM_JOB_NAME $SLURM_JOB_ID $SLURMD_NODENAME $SLURM_ARRAY_TASK_ID" echo "---------------" if [[ -z "${SLURM_ARRAY_TASK_ID}" ]]; then echo "Not operating within an array" exit 1 fi - -if [[ "${SLURM_ARRAY_TASK_MIN}" -ne 1 ]]; then - echo "Min array ID is not 1" - exit 1 -fi if [[ -z ${MMI} ]]; then echo "MMI is not set" exit 1 @@ -56,11 +51,7 @@ fi # DO NOT do this casually. Only do a clean up like this if # you know for sure TMPDIR is what you want. -# we might got back to this TMPDIR once the slurm scheduler controls it -# TMPDIR=/dev/shm -# right now, let's use ${OUTPUT}, note that each worker will create a new tmp -# folder two lines below -TMPDIR=${OUTPUT} +TMPDIR=/dev/shm export TMPDIR=${TMPDIR} export TMPDIR=$(mktemp -d) echo $TMPDIR