UNIBE_IBU Configuration

Configuration file to run nf-core pipelines on the cluster of the Interfaculty Bioinformatics Unit of the University of Bern.

To use, run the pipeline with -profile unibe_ibu. This will download and launch the profile.config which has been pre-configured with a setup suitable for the IBU 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. This requires a local installation of singularity. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node.

Config file

See config file on GitHub

params {
    config_profile_description = "University of Bern, Interfaculty Bioinformatics Unit cluster profile"
    config_profile_contact = "irene.keller@dbmr.unibe.ch; info@bioinformatics.unibe.ch"
    config_profile_url = "https://www.bioinformatics.unibe.ch/"
    max_memory = 500.GB
    max_cpus = 128
    max_time = 240.h
process {
    executor = "slurm"
    maxRetries = 2
    beforeScript = 'mkdir -p ./tmp/ && export TMPDIR=./tmp/'
executor {
    queueSize = 30
singularity {
    enabled = true
    autoMounts = true