diff --git a/src/nextflow.pbs b/src/nextflow.pbs deleted file mode 100644 index e89d8599f10aeac03270e3b1b26d9a376edf7a15..0000000000000000000000000000000000000000 --- a/src/nextflow.pbs +++ /dev/null @@ -1,39 +0,0 @@ -#! /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/"