src/ cleanup .pbs example

src/nextflow.pbs

-#! /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/"