diff --git a/singularity/run_pipeline.sh b/singularity/run_pipeline.sh index 32bff4d2b2644794ead47db13dba9130707d2188..c3485ce7844ba27c60d8356885986732a6bf6d1c 100755 --- a/singularity/run_pipeline.sh +++ b/singularity/run_pipeline.sh @@ -110,7 +110,7 @@ fi [[ ${QOS} ]] || QOS="normal" [[ ${PART} ]] || PART="common" -batch_cmd="sbatch --mem={cluster.ram} --cpus-per-task={threads} --job-name={rule}-{wildcards} --qos=${QOS} --part=${PART} ${wrapper} ${container}" +sbatch_cmd="sbatch --mem={cluster.ram} --cpus-per-task={threads} --job-name={rule}-{wildcards} --qos=${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}"