GenOuest Configuration

All nf-core pipelines have been successfully configured for use on the GenOuest cluster.

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

Running the workflow on the GenOuest cluster

Nextflow is installed on the GenOuest cluster. Some documentation is available on the GenOuest website.

You need to activate it like this (or any more recent version in the same directory):

source /local/env/envnextflow-22.10.4.sh

Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command. Nextflow shouldn’t run directly on the submission node but on a compute node. Run nextflow from a compute node:

# Login to a compute node
srun --pty bash
 
# Load the dependencies if not done before
source /local/env/envnextflow-22.10.4.sh
 
# Run a downloaded/git-cloned nextflow workflow from
nextflow run \\
/path/to/nf-core/workflow \\
-resume
-profile genouest \\
--email my-email@example.org  \\
-c my-specific.config
...
 
# Or use the nf-core client
nextflow run nf-core/rnaseq ...

Config file

See config file on GitHub

genouest.config
//Profile config names for nf-core/configs
params {
  config_profile_description = 'The GenOuest cluster profile'
  config_profile_contact = 'Anthony Bretaudeau (@abretaud)'
  config_profile_url = 'https://www.genouest.org'
}
 
singularity {
  enabled = true
  autoMounts = true
  runOptions = '-B /scratch:/scratch -B /local:/local -B /db:/db -B /groups:/groups'
}
 
process {
  executor = 'slurm'
}
 
params {
  igenomes_ignore = true
  igenomesIgnore = true //deprecated
  max_memory = 3000.GB
  max_cpus = 160
  max_time = 336.h
}