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Verified Commit 8d5f0314 authored by Laurent Modolo's avatar Laurent Modolo
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clarify example.pbs

parent 8a6217da
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...@@ -15,15 +15,23 @@ ...@@ -15,15 +15,23 @@
#$ -l sps=1 ## acces /sps directory #$ -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_VERSION=19.04
NF=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow NF=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
# change to your username PIPELINE=${SCRATCH}/${PROJECT}/src/${PIPELINE}.nf
SCRATCH=/sps/lbmc/<user>/ CONFIG=${SCRATCH}/${PROJECT}/src/${PIPELINE}.config
# change to your project / pipeline !
PIPELINE=${SCRATCH}/<project>/src/<pipeline>.nf
# change to your project / pipeline !
CONFIG=${SCRATCH}/<project>/src/<pipeline>.config
${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \ ${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \
--fasta "${SCRATCH}/<project>/data/fasta" \ --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"
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