nf-core/configs: BioHPC Genomics (BIOHPC_GEN) Configuration

All nf-core pipelines have been successfully configured for use on the BioHPC Genomics (biohpc_gen) cluster that is housed at the Leibniz Rechenzentrum (LRZ) for research groups at the Faculty of Biology of the Ludwig-Maximilians-University (LMU) in Munich.

To use, run the pipeline with -profile biohpc_gen. This will download and launch the biohpc_gen.config which has been pre-configured with a setup suitable for the biohpc_gen cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.

NB: You will need an account to use the LRZ Linux cluster as well as group access to the biohpc_gen cluster in order to run nf-core pipelines.

To correctly submit jobs into the biohpc_gen cluster the SLURM_CLUSTERS variable needs to be set:

export SLURM_CLUSTERS=biohpc_gen

We recommend using nextflow >= 25.04.2 and apptainer (1.3.4). These are then available as modules (please confirm the module name using module avail):

## Load Nextflow and apptainer environment modules
module load nextflow/25.04.2 apptainer/1.3.4

NB: bioHPC compute nodes are submit hosts. This means you can submit the nextflow head job via sbatch.

NB: Sometimes you may want to have jobs submitted ‘locally’ in a large nextflow job. Details on this can be found here https://doku.lrz.de/nextflow-on-hpc-systems-test-operation-788693597.html

Config file

See config file on GitHub

conf/biohpc_gen
//Profile config names for nf-core/configs
params {
    config_profile_description = 'BioHPC Genomics (biohpc_gen) cluster profile provided by nf-core/configs'
    config_profile_contact     = 'Niklas Schandry (@nschan)'
    config_profile_url         = 'https://collab.dvb.bayern/display/LMUBioHPCGenomics/BioHPC+Genomics'
}


process {
        resourceLimits = [
            memory: 3.TB,
            cpus: 80,
            time: 14.d
        ]
    executor       = 'slurm'
    queue          = { task.memory <= 1536.GB ? (task.time > 2.d || task.memory > 384.GB ? 'biohpc_gen_production' : 'biohpc_gen_normal') : 'biohpc_gen_highmem' }
    clusterOptions = '--clusters=biohpc_gen'
    array = 25
}


executor {
    $slurm {
        queueStatInterval = '10 min'
        pollInterval = '30 sec'
        submitRateLimit = '25sec'
    }
}


apptainer {
    enabled   = true
    autoMounts = true
}