diff --git a/src/nextflow.pbs b/src/nextflow.pbs index 80bb9f89abddcfe565f4d2de675e3e1daff86344..d1fede85c35396fd869d18b90003aad77a4491f1 100644 --- a/src/nextflow.pbs +++ b/src/nextflow.pbs @@ -6,21 +6,20 @@ #$ -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 ! +#$ -o /sps/lbmc/<user>/logs/ # change to your username ! +#$ -e /sps/lbmc/<user>/logs/ # change to your username ! #$ -r n # relaunch y/n -#$ -M laurent.modolo@ens-lyon.fr +#$ -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=/pbs/throng/lbmc/cl7/nextflow/19.04/nextflow +NF_VERSION=19.04 +NF=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow PIPELINE=/sps/lbmc/common/nextflow/src/nf_modules/kallisto/indexing.nf CONFIG=/sps/lbmc/common/nextflow/src/nf_modules/kallisto/indexing.config -$NF \ -$PIPELINE \ --c $CONFIG \ --profile ccin2p3_conda \ ---fasta "/sps/lbmc/common/nextflow/data/tiny_dataset/fasta/tiny_v2.fasta" +${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \ +--fasta "/sps/lbmc/common/nextflow/data/tiny_dataset/fasta/tiny_v2.fasta" \ +-w "/sps/lbmc/<user>/"