Quoting issue.

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} $@"