Running MPRAflow on HPC Cluster

Nextflow gives us the opportunity to run MPRAflow in a cluster environment. Right now we split up processes into two main groups: longtime and shorttime. We can define different job setting for both groups. As you can imagine from the names longtime defines processes that takes a while when running. Sometimes several days. shortime defines processes that are quicker and are usually done in several minutes.

To enable the submission to your cluster you have to edit the conf/cluster.config, allowing each process to be run as a separate qsub, sbatch or similar command. The config contains example code for SGE, LSF, and SLURM architectures. Please remove the \ for the architecture you would like to use and place \ in front of any architectures not currently in use. A \ in front of all of them runs the pipeline on your local machine (default). If you run MPRAflow on a cluster system make sure be that you export all environment variables. E.g. this can be done with the -V option by SGE.

Note

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