diff options
| author | Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk> | 2024-11-14 12:38:30 +0000 |
|---|---|---|
| committer | Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk> | 2024-11-14 12:38:30 +0000 |
| commit | 7550d95074c0eb4dd365d6dc2540b07c0066e5d2 (patch) | |
| tree | a217010c7aef7ece6d2cc819c910e7d946944637 /pilot.sh | |
| parent | 381140763bdbe9d20ae91e55cac5010d93c7f08d (diff) | |
Correct syntax in variable setting
Diffstat (limited to 'pilot.sh')
| -rw-r--r-- | pilot.sh | 16 |
1 files changed, 8 insertions, 8 deletions
@@ -53,14 +53,14 @@ INPUT_DIR="${2}" PIPELINE_LOG="${HOME}/${WORKFLOW_NAME}.log" -TMP_OUTDIR="${OUTDIR-$INPUT_DIR}/toil/tmp/tmp/" -JOB_LOG_DIR="${OUTDIR-$INPUT_DIR}/toil/logs/" -BATCH_LOG_DIR="${OUTDIR-$TOIL_BATCH_LOGS_DIR:-${INPUT_DIR}/toil/logs}" -WORK_DIR="${OUTDIR-$INPUT_DIR}/toil/work/" - -OUTPUT_DIR="${OUTDIR-$INPUT_DIR}/${WORKFLOW_NAME}_results" -JOBSTORE_DIR="${OUTDIR-$INPUT_DIR}/toil/${WORKFLOW_NAME}_job/" -STATS_DIR="${OUTDIR-$OUTPUT_DIR}/stats" +TMP_OUTDIR="${OUTDIR:-$INPUT_DIR}/toil/tmp/tmp/" +JOB_LOG_DIR="${OUTDIR:-$INPUT_DIR}/toil/logs/" +BATCH_LOG_DIR="${TOIL_BATCH_LOGS_DIR:-${OUTDIR}/toil/logs}" +WORK_DIR="${OUTDIR:-$INPUT_DIR}/toil/work/" + +OUTPUT_DIR="${OUTDIR:-$INPUT_DIR}/${WORKFLOW_NAME}_results" +JOBSTORE_DIR="${OUTDIR:-$INPUT_DIR}/toil/${WORKFLOW_NAME}_job/" +STATS_DIR="${OUTDIR:-$OUTPUT_DIR}/stats" mkdir -p "$JOB_LOG_DIR" mkdir -p "$BATCH_LOG_DIR" |