Maestro (at Pateur Institute, Paris) Configuration

To use, run the pipeline with -profile maestro,<qos> (with qos being long or normal). This will download and launch the maestro.config which has been pre-configured with a setup suitable for the Maestro cluster on either the long or normal qos. Using one of these profiles, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline

needed Modules

Please first load java, nextflow and singularity modules module load java module load nextflow module load singularity

Also, do not forget to run nextflow using tmux or alike.

Other profiles at Pasteur

If you are using TARS cluster, please refer to the pasteur profile.

Please refer to docs/pasteur.md for installing and running nf-core instructions.

Config file

See config file on GitHub

maestro.config
params {
  config_profile_description = 'Institut Pasteur Maestro cluster profile'
  config_profile_url = 'https://research.pasteur.fr/en/equipment/maestro-compute-cluster/'
  config_profile_contact = 'Pierre Luisi (@pierrespc)'
}
 
singularity {
  enabled = true
  autoMounts = true
  runOptions = '--home $HOME:/home/$USER --bind /pasteur'
}
 
profiles {
    
    normal {
        process {
              executor = 'slurm'
              scratch = false
              queue = 'common'
              queueSize = 20
              clusterOptions = '--qos=normal'
        }
 
        params {
            igenomes_ignore = true
            igenomesIgnore = true
            max_memory = 500.GB
            max_cpus = 96
            max_time = 24.h
        }
    }
 
    long {
        process {
              executor = 'slurm'
              scratch = false
              queue = 'long'
              clusterOptions = '--qos=long -p long'
        }
 
        params {
            igenomes_ignore = true
            igenomesIgnore = true
            max_memory = 500.GB
            max_cpus = 5
            max_time = 8760.h
        }
    }
 
}