Section for Evolutionary Genomics at GLOBE, Univeristy of Copenhagen (hologenomics partition on HPC) Configuration

NB: You will need an account to use the HPC cluster to run the pipeline. If in doubt contact IT.

The profile is configured to run with Singularity version 3.6.3-1.el7 which is part of the OS installtion and does not need to be loaded as a module.

Before running the pipeline you will need to load Java, miniconda and Nextflow. You can do this by including the commands below in your SLURM/sbatch script:

## Load Java and Nextflow environment modules
module purge
module load lib
module load java/v1.8.0_202-jdk miniconda nextflow/v20.07.1.5412

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 completeed successfully. If the run does not complete successfully then the work/ dir should be removed manually to save storage space.

This configuration will automatically choose the correct SLURM queue (short,medium,long) depending on the time and memory required by each process.

NB: Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be submitted from one of the login nodes.

Config file

See config file on GitHub

//Profile config names for nf-core/configs
params {
    config_profile_description = 'Section for Evolutionary Genomics @ GLOBE, University of Copenhagen - seg_globe profile provided by nf-core/configs.'
    config_profile_contact = 'Aashild Vaagene (@ashildv)'
    config_profile_url = ''
    max_memory = 250.GB
    max_cpus = 35
    max_time = 720.h
singularity {
    enabled = true
    autoMounts = true
    cacheDir = '/shared/volume/hologenomics/data/cache/nf-eager/singularity'
process {
    executor = 'slurm'
    queue = { task.time < 24.h ? 'hologenomics-short' : task.time < 168.h ? 'hologenomics' : 'hologenomics-long' }
cleanup = true
executor {
    queueSize = 8