diff --git a/singularity/run_pipeline.sh b/singularity/run_pipeline.sh index ddb47de346cc971e23c8197c67d312cc3398264e..32bff4d2b2644794ead47db13dba9130707d2188 100755 --- a/singularity/run_pipeline.sh +++ b/singularity/run_pipeline.sh @@ -110,7 +110,8 @@ fi [[ ${QOS} ]] || QOS="normal" [[ ${PART} ]] || PART="common" -cluster_opts="--cluster \\\'sbatch --mem={cluster.ram} --cpus-per-task={threads} --job-name={rule}-{wildcards} --qos=${QOS} --part=${PART} ${wrapper} ${container}\\\' --cluster-config ${cluster_config}" +batch_cmd="sbatch --mem={cluster.ram} --cpus-per-task={threads} --job-name={rule}-{wildcards} --qos=${QOS} --part=${PART} ${wrapper} ${container}" +cluster_opts="--cluster \'${sbatch_cmd}\' --cluster-config ${cluster_config}" #cluster_opts="--cores 20 --cluster \'sbatch --mem={cluster.ram} --cpus-per-task={threads} --job-name={rule}-{wildcards} --qos=${QOS} --part=${PART} --mpi=none\' -j 300" #cmd="APPTAINERENV_USER=${USER} apptainer run --cleanenv -B /opt/hpc/slurm -B /var/run/munge -B /pasteur ${container} ${PROGNAME} ${pipeline_config} ${cluster_opts} --cluster-config ${cluster_config}" #cmd="APPTAINERENV_USER=${USER} apptainer run --cleanenv -B /opt/hpc/slurm -B /var/run/munge -B /pasteur ${container} ${PROGNAME} $@"