nf-core/configs: 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 (one hyphen). This requires a local installation of singularity, so you have to run the pipeline from a compute node.

For accounting, you can specify an IBU project id with the —project flag (two hyphens) when launching Nextflow. If no project is specified, it will default to the username.

Config file

See config file on GitHub

conf/unibe_ibu
params {
    config_profile_description = "University of Bern, Interfaculty Bioinformatics Unit cluster profile"
    config_profile_contact     = "alexander.nater@unibe.ch; info@bioinformatics.unibe.ch"
    config_profile_url         = "https://www.bioinformatics.unibe.ch/"
    schema_ignore_params       = "project,clusterOptions"
    project                    = null
    clusterOptions             = null
}
 
validation {
    ignoreParams = ["schema_ignore_params", "project", "clusterOptions"]
}
 
process {
    resourceLimits = [
        memory: 500.GB,
        cpus: 128,
        time: 672.h
    ]
    executor       = 'slurm'
    queue          = 'pibu_el8'
    maxRetries     = 2
    scratch        = '$SCRATCH'
    clusterOptions = (params.project ? "-A ${params.project} " : '') + "${params.clusterOptions ?: ''}"
}
 
executor {
    queueSize = 50
}
 
singularity {
    enabled    = true
    autoMounts = true
}