From 05725c46cd33d72db60d5ea5954541f073163dec Mon Sep 17 00:00:00 2001
From: Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk>
Date: Tue, 8 Jul 2025 16:12:51 -0400
Subject: Expose the batching system

The queuing system was hard-coded to slurm. It may be, at times,
convenient to be able to run workflows on the local node (or use
a different queuing system altogether).

The old behaviour is maintained by setting the batching system
to slurm by default; the user can change the system by using
--batch_system.
---
 pilot.sh | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

(limited to 'pilot.sh')

diff --git a/pilot.sh b/pilot.sh
index 736f9a2..61e02af 100644
--- a/pilot.sh
+++ b/pilot.sh
@@ -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} \
-- 
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