diff options
Diffstat (limited to 'pilot.sh')
| -rw-r--r-- | pilot.sh | 8 |
1 files changed, 5 insertions, 3 deletions
@@ -1,7 +1,7 @@ #!/bin/sh -eu usage() { - echo "Usage: ${PROGRAM} [-r|--restart] [-h|--help] [-c|--container <singularity container>] [--scratch <scratch dir>] [--outdir <output dir>] (-f <input file>) (-p <pipeline>) <Workflow> <input dir>" + echo "Usage: ${PROGRAM} [-r|--restart] [-h|--help] [-c|--container <singularity container>] [--scratch <scratch dir>] [--outdir <output dir>] [--batch_system <batch system>] (-f <input file>) (-p <pipeline>) <Workflow> <input dir>" exit 0 } @@ -19,13 +19,14 @@ set_container() { fi } -opts=$(getopt -o rhf:c:p: --long restart,help,container:,scratch:,outdir: \ +opts=$(getopt -o rhf:c:p: --long restart,help,container:,scratch:,outdir:,batch_system: \ -n 'pilot' -- "$@") eval set -- "$opts" RESTART="" SCRATCH="" +BATCH_SYSTEM="slurm" while true; do case "$1" in -c | --container) set_container "${2}"; shift 2 ;; @@ -35,6 +36,7 @@ while true; do -r | --restart) RESTART="--restart"; shift ;; --scratch) SCRATCH="${2}"; shift 2 ;; --outdir) OUTDIR="${2}"; shift 2;; + --batch_system) BATCH_SYSTEM="${2}"; shift 2;; * ) shift; break ;; esac done @@ -99,7 +101,7 @@ TOIL_COMMAND="toil-cwl-runner ${RESTART} ${TMPDIR_PREFIX} \ --writeLogs ${JOB_LOG_DIR} \ --stats \ --clusterStats ${STATS_DIR} \ - --batchSystem slurm \ + --batchSystem ${BATCH_SYSTEM} \ --batchLogsDir ${BATCH_LOG_DIR} \ --tmp-outdir-prefix ${TMP_OUTDIR} \ --workDir ${WORK_DIR} \ |