From 9e5334d83599cdef09f180c3f0411d6cf9b97e7e Mon Sep 17 00:00:00 2001
From: Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk>
Date: Mon, 28 Oct 2024 16:13:40 +0000
Subject: Add option to specify a separate output directory

---
 pilot.sh | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

(limited to 'pilot.sh')

diff --git a/pilot.sh b/pilot.sh
index b41f6fd..d497415 100644
--- a/pilot.sh
+++ b/pilot.sh
@@ -18,7 +18,7 @@ set_container() {
     fi
 }
 
-opts=$(getopt -o rhf:c:p: --long restart,help,container:,scratch: \
+opts=$(getopt -o rhf:c:p: --long restart,help,container:,scratch:,outdir: \
         -n 'pilot' -- "$@")
 
 eval set -- "$opts"
@@ -33,6 +33,7 @@ while true; do
         -p ) PIPELINE="${2}"; shift 2 ;;
         -r | --restart) RESTART="--restart";    shift ;;
         --scratch) SCRATCH="${2}"; shift 2 ;;
+        --outdir) OUTDIR="${2}"; shift 2;;
         * ) shift; break ;;
     esac
 done
@@ -52,14 +53,14 @@ INPUT_DIR="${2}"
 
 PIPELINE_LOG="${HOME}/${WORKFLOW_NAME}.log"
 
-TMP_OUTDIR="${INPUT_DIR}/toil/tmp/tmp/"
-JOB_LOG_DIR="${INPUT_DIR}/toil/logs/"
-BATCH_LOG_DIR="${TOIL_BATCH_LOGS_DIR:-${INPUT_DIR}/toil/logs}"
-WORK_DIR="${INPUT_DIR}/toil/work/"
-# TODO: optionally decouple output directory from input directory?
-OUTPUT_DIR="${INPUT_DIR}/${WORKFLOW_NAME}_results"
-JOBSTORE_DIR="${INPUT_DIR}/toil/${WORKFLOW_NAME}_job/"
-STATS_DIR="${OUTPUT_DIR}/stats"
+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"
 
 mkdir -p "$JOB_LOG_DIR"
 mkdir -p "$BATCH_LOG_DIR"
-- 
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