From e25a64b92095bdf0506fc7797a276803179029ee Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 22 May 2019 15:18:27 +0200
Subject: [PATCH] nextflow.pbs: fix pbs example

---
 src/nextflow.pbs | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/nextflow.pbs b/src/nextflow.pbs
index 397dbf98..1f5a2bdf 100644
--- a/src/nextflow.pbs
+++ b/src/nextflow.pbs
@@ -25,11 +25,11 @@ PIPELINE=<pipeline_name>
 NF_VERSION=19.04
 
 
-NF=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
-PIPELINE=${SCRATCH}/${PROJECT}/src/${PIPELINE}.nf
+NEXTFLOW=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
+NF=${SCRATCH}/${PROJECT}/src/${PIPELINE}.nf
 CONFIG=${SCRATCH}/${PROJECT}/src/${PIPELINE}.config
 
-${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \
+${NEXTFLOW} ${NF} -c ${CONFIG} -profile ccin2p3 \
 --fasta "${SCRATCH}/<project>/data/fasta" \
 -w "${SCRATCH}/${PROJECT}/work/" \
 -with-report "${SCRATCH}/${PROJECT}/results/${PIPELINE}_report.html" \
-- 
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