CCGA DX Configuration

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

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

Before running the pipeline you will need to have Nextflow installed.

NB: Access to the CCGA DX cluster is restricted to IKMB/CCGA employes. Please talk to Marc Hoeppner to get access (@marchoeppner).

Config file

See config file on GitHub

//Profile config names for nf-core/configs
params {
    config_profile_description = 'CCGA DX cluster profile provided by nf-core/configs.'
    config_profile_contact = 'Marc Hoeppner (@marchoeppner)'
    config_profile_url = ''
 * -------------------------------------------------
 *  Nextflow config file for CCGA cluster in Kiel
 * -------------------------------------------------
singularity {
    enabled = true
    runOptions = "-B /mnt -B /work_ifs"
executor {
process {
    // Global process config
    executor = 'slurm'
    queue = 'htc'
params {
    // illumina iGenomes reference file paths on DX Cluster
    igenomes_base = '/work_ifs/ikmb_repository/references/iGenomes/references/'
    saveReference = true
    max_memory = 250.GB
    max_cpus = 20
    max_time = 240.h