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 using following command sinfo --cluster wice|genius.
Before running the pipeline you will need to create a slurm script that acts as a master script to submit all jobs.
$ more job.pbs
#!/bin/bash
#SBATCH --account=...
#SBATCH --chdir=....
#SBATCH --partition=batch_long
#SBATCH --nodes="1"
#SBATCH --ntasks-per-node="1"
module load Nextflow
nextflow run <pipeline> -profile vsc_kul_uhasselt,<CLUSTER> --project <your-credential-acc> <Add your other parameters>NB: You have to specify your credential account, else the jobs will fail!
Here the cluster options are:
- genius
- wice
- superdome
NB: The vsc_kul_uhasselt profile is based on a selected amount of SLURM partitions. Should you require resources outside of these limits (e.g. more memory or gpus) you will need to provide a custom config specifying an appropriate SLURM partition (e.g. 'bigmem*', or 'gpu*').
Use the --cluster option to specify the cluster you intend to use when submitting the job:
sbatch --cluster=wice|genius job.slurm 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 $VSC_SCRATCH/work per this configuration
NB: The default directory where the
work/andsingularity/(cache directory for images) is located in$VSC_SCRATCH.