Sarek/nextflow.config at 5a6406d1c963836e64f81f24e27035c29d03c5dd · KochTobi/Sarek · 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 {
  homePage = 'http://opensource.scilifelab.se/projects/sarek/'
  description = 'Sarek - Workflow For Somatic And Germline Variations'
}

env {
  NXF_OPTS="-Xms1g -Xmx4g"
}

profiles {
  // Default profile for UPPMAX secure clusters
  // Runs the pipeline locally on a single 16-core node
  // Singularity images need to be set up
  standard {
    includeConfig 'configuration/base.config'
    includeConfig 'configuration/uppmax-localhost.config'
    includeConfig 'configuration/singularity-path.config'
  }
  // slurm profile for UPPMAX secure clusters
  // Runs the pipeline using the job scheduler
  // Singularity images need to be set up
  slurm {
    includeConfig 'configuration/base.config'
    includeConfig 'configuration/uppmax-slurm.config'
    includeConfig 'configuration/singularity-path.config'
  }
  // slurm profile for UPPMAX clusters
  // Runs the pipeline using the job scheduler
  // Singularity images will be pulled automatically
  slurmDownload {
    includeConfig 'configuration/base.config'
    includeConfig 'configuration/uppmax-slurm.config'
    includeConfig 'configuration/singularity.config'
    includeConfig 'configuration/containers.config'
  }
  // Small testing with Docker profile
  // Docker images will be pulled automatically
  docker {
    includeConfig 'configuration/base.config'
    includeConfig 'configuration/travis.config'
    includeConfig 'configuration/docker.config'
    includeConfig 'configuration/containers.config'
  }
  // AWS Batch with Docker profile
  // Docker images will be pulled automatically
  awsbatch {
    includeConfig 'configuration/base.config'
    includeConfig 'configuration/aws-batch.config'
    includeConfig 'configuration/docker.config'
    includeConfig 'configuration/containers.config'
  }
  // Small testing with Singularity profile
  // Singularity images will be pulled automatically
  singularity {
    includeConfig 'configuration/base.config'
    includeConfig 'configuration/travis.config'
    includeConfig 'configuration/singularity.config'
    includeConfig 'configuration/containers.config'
  }
  // Small testing with Singularity profile
  // Singularity images need to be set up
  singularityPath {
    includeConfig 'configuration/base.config'
    includeConfig 'configuration/travis.config'
    includeConfig 'configuration/singularity-path.config'
  }

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