IMB Configuration

All nf-core pipelines have been successfully configured for use on the HPC system at the Institute of Molecular Biology (IMB) in Mainz / Germany.

To use this profile, run the pipeline with -profile imb. This will download and launch the imb.config which has been pre-configured with a setup suitable for the IMB HPC system. Using this profile, container images with all required software will be downloaded before execution of the pipeline.

Before running the pipeline, you will need to load Nextflow using the environment module system on the IMB HPC system. You can do this by issuing the command below:

module load nextflow

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

Config file

See config file on GitHub

params {
    config_profile_description    = 'Institute of Molecular Biology (IMB) HPC cluster profile provided by nf-core/configs'
    config_profile_contact        = 'Patrick Hüther (@phue)'
    config_profile_url            = ''
    config_profile_name           = 'IMB HPC cluster'
    max_cpus   = 32
    max_memory = 1.TB
    max_time   = 7.d
singularity {
    enabled    = true
    autoMounts = true
executor {
    name      = 'slurm'
    jobName   = { "${task.process.split(':').last()}" }
    queueSize = 20
process {
    scratch = '/jobdir/$SLURM_JOB_ID'
    cache   = 'lenient'
    queue   = "groups".execute().text.contains('imb-bioinfocf')
            ? { task.time <= 5.h ? 'bcfshort' : 'bcflong' }
            : { task.time <= 5.h ? 'short' : 'long' }