nf-core/configs: CCGA CAU Cluster Configuration

Deployment and testing of nf-core pipelines at the CCGA cau cluster is on-going.

To use, run the pipeline with -profile ccga_cau. This will download and launch the ccga_cau.config which has been pre-configured with a setup suitable for the caucluster. 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.

Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on the cluster. You can do this by issuing the commands below:

## Load Nextflow and Singularity environment modules
module load gcc12-env
module load nextflow
module load singularity

NB: Access to the caucau cluster is restricted. Please talk to Georg Hemmrich-Stanisak to get access (@ghemmrich).

Config file

See config file on GitHub

conf/ccga_cau
//Profile config names for nf-core/configs
params {
    config_profile_description = 'CCGA CAU cluster profile provided by nf-core/configs.'
    config_profile_contact     = 'OlgaBrovkina (@brovolia)'
    config_profile_url         = 'https://www.ccga.uni-kiel.de/'
}
 
/*
 * -------------------------------------------------
 *  Nextflow config file for CAU cluster in Kiel
 * -------------------------------------------------
 */
 
singularity {
    enabled    = true
    autoMounts = true
    cacheDir   = "/work_ikmb/ikmb_repository/singularity_cache/"
}
 
executor {
    queueSize = 100
}
 
process {
    resourceLimits = [
        memory: 250.GB,
        cpus: 24,
        time: 120.h
    ]
 
    // Global process config
    executor = 'slurm'
    queue    = 'base'
}
 
params {
    // illumina iGenomes reference file paths on RZCluster
    igenomes_base = '/work_ikmb/ikmb_repository/references/iGenomes/references/'
    saveReference = true
    max_memory    = 250.GB
    max_cpus      = 24
    max_time      = 120.h
}