Section for Hologenomics at GLOBE, University of Copenhagen (Mjolnir server) Configuration

NB: You will need an account on Mjolnir to run the pipeline. If in doubt contact IT.

Prior to running the pipeline for the first time with the mjolnir_globe.config (../conf/mjolnir_globe.config), users must create a hidden directory called .tmp_nfcore in their data/project directory on Mjolnir where the temp files from nf-core pipelines will be re-directed by the NXF_TEMP command (see below).

The contents of the .tmp_nfcore directory should be periodically deleted manually to save on space. If the NXF_TEMP command is not used to properly re-direct temp files the /tmp directory on the compute nodes will be used and quickly filled up, which blocks anyone from working on these nodes until the offending user removes their files.

The following lines must be added by users to their ~/.bash_profile:

#re-direct tmp files away from /tmp directories on compute nodes or the headnode
export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_nfcore
# nextflow - limiting memory of virtual java machine
NXF_OPTS='-Xms1g -Xmx4g'

Once you have created the .tmp_nfcore directory and added the above lines of code to your .bash_profile you can run an nf-core pipeline.

Before running a pipeline you will need to load Java, Miniconda, Singularity 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 jdk/1.8.0_291 miniconda singularity/3.8.0 nextflow/

All of the intermediate output 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 mjolnir_globe 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.

Config file

See config file on GitHub

//Profile config names for nf-core/configs
params {
    config_profile_description = 'Section for Hologenomics and Section for Molecular Ecology and Evolution @ Globe Institute, University of Copenhagen - mjolnir_globe profile provided by nf-core/configs.'
    config_profile_contact = 'Bent Petersen (@bentpetersendk)'
    config_profile_url = ''
    max_memory = 750.GB
    max_cpus = 50
    max_time = 336.h
singularity {
        enabled = true
        autoMounts = true
        cacheDir = '/maps/projects/mjolnir1/data/cache/nf-core/singularity'
process {
    executor = 'slurm'
cleanup = true
executor {
    queueSize = 10