From 3650829c30da9ff6a8a57f248cf11ea523f5cb4f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 7 May 2019 11:35:01 +0200
Subject: [PATCH] nextflow.pbs: working qsub for ccin2p3
---
src/nextflow.pbs | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/src/nextflow.pbs b/src/nextflow.pbs
index 80bb9f89..d1fede85 100644
--- a/src/nextflow.pbs
+++ b/src/nextflow.pbs
@@ -6,21 +6,20 @@
#$ -l demon=1
#$ -P P_lbmc
#$ -N nf_pipe
-#$ -o /sps/lbmc/lmodolo/logs/ # change to your username !
-#$ -e /sps/lbmc/lmodolo/logs/ # change to your username !
+#$ -o /sps/lbmc/<user>/logs/ # change to your username !
+#$ -e /sps/lbmc/<user>/logs/ # change to your username !
#$ -r n # relaunch y/n
-#$ -M laurent.modolo@ens-lyon.fr
+#$ -M <email>@ens-lyon.fr # change to your mail !
#$ -m be ## send an email when the job starts and ends
#$ -l os=cl7 ## choose OS
#$ -l sps=1 ## acces /sps directory
#####################################
-NF=/pbs/throng/lbmc/cl7/nextflow/19.04/nextflow
+NF_VERSION=19.04
+NF=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
PIPELINE=/sps/lbmc/common/nextflow/src/nf_modules/kallisto/indexing.nf
CONFIG=/sps/lbmc/common/nextflow/src/nf_modules/kallisto/indexing.config
-$NF \
-$PIPELINE \
--c $CONFIG \
--profile ccin2p3_conda \
---fasta "/sps/lbmc/common/nextflow/data/tiny_dataset/fasta/tiny_v2.fasta"
+${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \
+--fasta "/sps/lbmc/common/nextflow/data/tiny_dataset/fasta/tiny_v2.fasta" \
+-w "/sps/lbmc/<user>/"
--
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