diff --git a/src/nextflow.pbs b/src/nextflow.pbs new file mode 100644 index 0000000000000000000000000000000000000000..aa3d9c0b602cbea6748d438b289dc51755ebf2dd --- /dev/null +++ b/src/nextflow.pbs @@ -0,0 +1,26 @@ +#!/bin/sh +##################################### +# job script example with GE options +##################################### +#$ -S "/usr/local/bin/bash -l" +#$ -q demon +#$ -P P_lbmc +#$ -N nf_pipe +#$ -o /sps/inter/lbmc/lmodolo/logs/ +#$ -e /sps/inter/lbmc/lmodolo/logs/ +#$ -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 +##################################### + +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 /pbs/throng/lbmc/cl7/nextflow/19.01/nextflow \ +-profile ccin2p3_conda \ +$PIPELINE \ +-c $CONFIG \ +$OPTIONS