From 787e9c423175a478903e00a2ff51b57a1cc1cb19 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 4 Jun 2019 09:59:07 +0200
Subject: [PATCH] nextflow.pbs: change position of NF option to facilitate bug
tracking
---
src/nextflow.pbs | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/src/nextflow.pbs b/src/nextflow.pbs
index 76eb7063..4aaff8e7 100644
--- a/src/nextflow.pbs
+++ b/src/nextflow.pbs
@@ -29,11 +29,11 @@ NEXTFLOW=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
NF=${SCRATCH}/${PROJECT}/src/${PIPELINE}.nf
CONFIG=${SCRATCH}/${PROJECT}/src/${PIPELINE}.config
DATA=${SCRATCH}/${PROJECT}/data
+NF_OPTIONS="-w \"${SCRATCH}/${PROJECT}/work/\" \
+-with-report \"${SCRATCH}/${PROJECT}/results/${PIPELINE}_report.html\" \
+-with-timeline \"${SCRATCH}/${PROJECT}/results/${PIPELINE}_timeline.html\" \
+-with-dag \"${SCRATCH}/${PROJECT}/results/${PIPELINE}_dag.pdf\""
-${NEXTFLOW} ${NF} -c ${CONFIG} -profile ccin2p3 \
+${NEXTFLOW} ${NF} -c ${CONFIG} -profile ccin2p3 ${NF_OPTIONS} \
--fasta "${DATA}/fasta" \
--results "${SCRATCH}/${PROJECT}/results/"
--w "${SCRATCH}/${PROJECT}/work/" \
--with-report "${SCRATCH}/${PROJECT}/results/${PIPELINE}_report.html" \
--with-timeline "${SCRATCH}/${PROJECT}/results/${PIPELINE}_timeline.html" \
--with-dag "${SCRATCH}/${PROJECT}/results/${PIPELINE}_dag.pdf"
--
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