Verified Commit bbc6d352 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

nextflow.pbs: give a hint that the results folder should be a parameter

of the pipe
parent e25a64b9
...@@ -28,9 +28,11 @@ NF_VERSION=19.04 ...@@ -28,9 +28,11 @@ NF_VERSION=19.04
NEXTFLOW=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow NEXTFLOW=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
NF=${SCRATCH}/${PROJECT}/src/${PIPELINE}.nf NF=${SCRATCH}/${PROJECT}/src/${PIPELINE}.nf
CONFIG=${SCRATCH}/${PROJECT}/src/${PIPELINE}.config CONFIG=${SCRATCH}/${PROJECT}/src/${PIPELINE}.config
DATA=${SCRATCH}/${PROJECT}/data
${NEXTFLOW} ${NF} -c ${CONFIG} -profile ccin2p3 \ ${NEXTFLOW} ${NF} -c ${CONFIG} -profile ccin2p3 \
--fasta "${SCRATCH}/<project>/data/fasta" \ --fasta "${DATA}/fasta" \
--results "${SCRATCH}/${PROJECT}/results/"
-w "${SCRATCH}/${PROJECT}/work/" \ -w "${SCRATCH}/${PROJECT}/work/" \
-with-report "${SCRATCH}/${PROJECT}/results/${PIPELINE}_report.html" \ -with-report "${SCRATCH}/${PROJECT}/results/${PIPELINE}_report.html" \
-with-timeline "${SCRATCH}/${PROJECT}/results/${PIPELINE}_timeline.html" \ -with-timeline "${SCRATCH}/${PROJECT}/results/${PIPELINE}_timeline.html" \
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