nf-configs/docs/vsc_ugent.md

nf-core/configs: University of Ghent High Performance Computing Infrastructure (VSC)

NB: You will need an account to use the HPC cluster to run the pipeline.

First you should go to the cluster you want to run the pipeline on. You can check what clusters have the most free space on this link. Use the following commands to easily switch between clusters:

module purge
module swap cluster/<CLUSTER>

Before running the pipeline you will need to create a PBS script to submit as a job.

#!/bin/bash

module load Nextflow

nextflow run <pipeline> -profile vsc_ugent,<CLUSTER> <Add your other parameters>

I also highly recommend specifying a location of a Singularity cache directory, by specifying the location with the $SINGULARITY_CACHEDIR bash environment variable in your .bash_profile or .bashrc or by adding it to your SLURM/PBS script. If this cache directory is not specified, the cache directory defaults to your $HOME/.singularity directory, which does not have a lot of disk space.

export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity

All of the intermediate files required to run the pipeline will be stored in the work/ directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the results/ directory anyway. The config contains a cleanup command that removes the work/ directory automatically once the pipeline has completed successfully. If the run does not complete successfully then the work/ dir should be removed manually to save storage space. The default work directory is set to $VSC_SCRATCH_VO_USER/work per this configuration

You can also add several TORQUE options to the PBS script. More about this on this link.

To submit your job to the cluster by using the following command:

qsub <script name>.pbs

NB: The profile only works for the clusters skitty, swalot, victini, kirlia and doduo.

NB: The default directory where the work/ and singularity (cache directory for images) is located in $VSC_SCRATCH_VO_USER.