From 7550d95074c0eb4dd365d6dc2540b07c0066e5d2 Mon Sep 17 00:00:00 2001
From: Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk>
Date: Thu, 14 Nov 2024 12:38:30 +0000
Subject: Correct syntax in variable setting

---
 pilot.sh | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

(limited to 'pilot.sh')

diff --git a/pilot.sh b/pilot.sh
index d497415..34d7009 100644
--- a/pilot.sh
+++ b/pilot.sh
@@ -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"
-- 
cgit v1.2.3