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
#####################################

NF_VERSION=19.04
NF=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
# change to your username
SCRATCH=/sps/lbmc/<user>/
# change to your project / pipeline !
PIPELINE=${SCRATCH}/<project>/src/<pipeline>.nf
# change to your project / pipeline !
CONFIG=${SCRATCH}/<project>/src/<pipeline>.config

${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \
--fasta "${SCRATCH}/<project>/data/fasta" \
-w "${SCRATCH}"