From bbc6d35256cc13bf5f7e5b746b8a28b16cd6ca35 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 22 May 2019 15:45:14 +0200
Subject: [PATCH] nextflow.pbs: give a hint that the results folder should be a
parameter of the pipe
---
src/nextflow.pbs | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/src/nextflow.pbs b/src/nextflow.pbs
index 1f5a2bdf..76eb7063 100644
--- a/src/nextflow.pbs
+++ b/src/nextflow.pbs
@@ -28,9 +28,11 @@ NF_VERSION=19.04
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
${NEXTFLOW} ${NF} -c ${CONFIG} -profile ccin2p3 \
---fasta "${SCRATCH}/<project>/data/fasta" \
+--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" \
--
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