Sarek_v2.2.1/nextflow.config at v2.2.1-blic · UCL-BLIC/Sarek_v2.2.1 · GitHub

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/*
 * -------------------------------------------------
 * Nextflow config file for Sarek
 * -------------------------------------------------
 * Default config options for all environments.
 * Cluster-specific config options should be saved
 * in the configuration folder and imported under a
 * profile name here.
 */


manifest {
  author = 'Szilvester Juhos, Maxime Garcia'
  description = 'Sarek - Workflow For Somatic And Germline Variations'
  homePage = 'http://sarek.scilifelab.se'
  mainScript = 'main.nf'
  name = 'Sarek'
  nextflowVersion = '>=0.32.0'
  version = '2.2.1'
}

env {
  NXF_OPTS="-Xms1g"
}

profiles {

  legion {
    includeConfig 'conf/legion.config'
    includeConfig 'conf/genomes_legion.config'
  }
  myriad {
    includeConfig 'conf/myriad.config'
    includeConfig 'conf/genomes_myriad.config'
  }
  myriad3 {
    includeConfig 'conf/myriad3.config'
    includeConfig 'conf/genomes_myriad.config'
  }

  // Small testing with Singularity profile
  // Singularity images will be pulled automatically
  singularity {
    includeConfig 'conf/base.config'
    includeConfig 'conf/travis.config'
    includeConfig 'conf/singularity.config'
    includeConfig 'conf/containers.config'
  }
  // Small testing with Singularity profile
  // Singularity images need to be set up
  singularityPath {
    includeConfig 'conf/base.config'
    includeConfig 'conf/travis.config'
    includeConfig 'conf/singularity-path.config'
  }

  // Default config for german BinAC cluster
  // Runs the pipeline using the pbs executor
  // Singularity images will be pulled automatically
  binac {
    includeConfig 'conf/base.config'
    includeConfig 'conf/binac.config'
    includeConfig 'conf/singularity.config'
    includeConfig 'conf/containers.config'
  }
}