#! /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/lmodolo/logs/ # change to your username !
#$ -e /sps/lbmc/lmodolo/logs/ # change to your username !
#$ -r n       # relaunch y/n
#$ -M laurent.modolo@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=19.10
NF=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
# change to your username
SCRATCH=/sps/lbmc/lmodolo/
# change to your project / pipeline !
PIPELINE=${SCRATCH}/nextflow/src/training_dataset.nf
# change to your project / pipeline !
CONFIG=${SCRATCH}/nextflow/src/training_dataset.config

${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \
--fasta "${SCRATCH}/nextflow/data/tiny_dataset/fasta/tiny_v2.fasta" \
--fastq_single "${SCRATCH}/nextflow/data/tiny_dataset/fastq/tiny2_S.fastq.gz" \
--chromosome "X" --start 5305683 --stop 5333928 -resume \
-w "${SCRATCH}"