From 8d5f031494f64147a3ff11b87ce9c3e6a1d6213c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 22 May 2019 10:01:12 +0200
Subject: [PATCH] clarify example.pbs
---
src/nextflow.pbs | 22 +++++++++++++++-------
1 file changed, 15 insertions(+), 7 deletions(-)
diff --git a/src/nextflow.pbs b/src/nextflow.pbs
index 4cb6e04c..397dbf98 100644
--- a/src/nextflow.pbs
+++ b/src/nextflow.pbs
@@ -15,15 +15,23 @@
#$ -l sps=1 ## acces /sps directory
#####################################
+# change to your username !
+SCRATCH=/sps/lbmc/<user>/
+# change to your project name !
+PROJECT=<project>
+#change to your project version !
+PIPELINE=<pipeline_name>
+#NF version to user
NF_VERSION=19.04
+
+
NF=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
-# change to your username
-SCRATCH=/sps/lbmc/<user>/
-# change to your project / pipeline !
-PIPELINE=${SCRATCH}/<project>/src/<pipeline>.nf
-# change to your project / pipeline !
-CONFIG=${SCRATCH}/<project>/src/<pipeline>.config
+PIPELINE=${SCRATCH}/${PROJECT}/src/${PIPELINE}.nf
+CONFIG=${SCRATCH}/${PROJECT}/src/${PIPELINE}.config
${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \
--fasta "${SCRATCH}/<project>/data/fasta" \
--w "${SCRATCH}"
+-w "${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"
--
GitLab