Unverified Commit 94a24ded authored by Laurent Modolo's avatar Laurent Modolo
Browse files

src/ cleanup .pbs example

parent 2835b4b2
#! /usr/local/bin/bash -l
#####################################
# job script example with GE options
#####################################
#$ -q demon
#$ -l demon=1
#$ -P P_lbmc
#$ -N nf_pipe
#$ -o /sps/lbmc/<user>/logs/ # change to your username !
#$ -e /sps/lbmc/<user>/logs/ # change to your username !
#$ -r n # relaunch y/n
#$ -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
#####################################
# 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
NEXTFLOW=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
NF=${SCRATCH}/${PROJECT}/src/${PIPELINE}.nf
CONFIG=${SCRATCH}/${PROJECT}/src/${PIPELINE}.config
DATA=${SCRATCH}/${PROJECT}/data
NF_OPTIONS="-w \"${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.html\""
${NEXTFLOW} ${NF} -c ${CONFIG} -profile ccin2p3 ${NF_OPTIONS} \
--fasta "${DATA}/fasta" \
--results "${SCRATCH}/${PROJECT}/results/"
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