Running MPRAsnakeflow on HPC Cluster

Snakemake gives us the opportunity to run MPRAsnakeflow in a cluster environment. Please check the Snakemake documentation for more information on how to set up a cluster environment. We already configured a cluster environment for SLURM. This can be used to adapt the workflow to other HPC environments.

The configuration (SLURM) of resources for rules can be found in config/sbatch.yml, allowing each process to be run as a separate sbatch command. For running MPRAsnakflow here is a possible command:

snakemake --use-conda --configfile conf/config.yaml --cluster "sbatch --nodes=1 --ntasks={cluster.threads} --mem={cluster.mem} -t {cluster.time} -p {cluster.queue} -o {cluster.output}" --jobs 100 --cluster-config config/sbatch.yaml

Please note that the log folder of the cluster environment has to be generated first, e.g:

mkdir -p logs


Please consult your cluster’s wiki page for cluster specific commands and change cluster Options to reflect these specifications. Additionally, for large libraries, more memory can be specified in this location.