#!/bin/sh
#####################################
# 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
#$ -m be      ## send an email when the job starts and ends
#$ -l os=cl7  ## choose OS
#$ -l sps=1   ## acces /sps directory
#####################################

NF=/pbs/throng/lbmc/cl7/nextflow/19.04/nextflow
PIPELINE=/sps/lbmc/common/nextflow/src/nf_modules/kallisto/indexing.nf
CONFIG=/sps/lbmc/common/nextflow/src/nf_modules/kallisto/indexing.config
OPTIONx="--fasta \"data/tiny_dataset/fasta/tiny_v2.fasta\""

time $NF \
-profile ccin2p3_conda \
$PIPELINE \
-c $CONFIG \
$OPTIONS