nextflow.config

/*
 * -------------------------------------------------
 * 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 = '2.3'
}

env {
  NXF_OPTS="-Xms1g"
}

profiles {
  // AWS Batch with Docker profile
  // Docker images will be pulled automatically
  awsbatch {
    includeConfig 'conf/base.config'
    includeConfig 'conf/aws-batch.config'
    includeConfig 'conf/docker.config'
    includeConfig 'conf/igenomes.config'
    includeConfig 'conf/resources.config'
    includeConfig 'conf/containers.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/igenomes.config'
    includeConfig 'conf/singularity.config'
    includeConfig 'conf/resources.config'
    includeConfig 'conf/containers.config'
  }
  // Default profile for BTB server
  // Runs the pipeline locally
  // Singularity images need to be set up
  btb {
    includeConfig 'conf/base.config'
    includeConfig 'conf/resources.config'
    includeConfig 'conf/munin.config'
    includeConfig 'conf/igenomes.config'
    includeConfig 'conf/singularity-path.config'
  }
  // Default config for CFC cluster in Tuebingen/Germany
  cfc {
    includeConfig 'conf/base.config'
    includeConfig 'conf/cfc.config'
    includeConfig 'conf/igenomes.config'
    includeConfig 'conf/singularity.config'
    includeConfig 'conf/resources.config'
    includeConfig 'conf/containers.config'
  }
  // Defines a conda environment.yml file in the current directory.
  // Careful when using it with other profiles as it might overwrite
  // the genomes/igenomes.config
  conda {
    includeConfig 'conf/base.config'
    includeConfig 'conf/travis.config'
    includeConfig 'conf/genomes.config'
    includeConfig 'conf/conda.config'
  }
  // Small testing with Docker profile
  // Docker images will be pulled automatically
  docker {
    includeConfig 'conf/base.config'
    includeConfig 'conf/travis.config'
    includeConfig 'conf/genomes.config'
    includeConfig 'conf/docker.config'
    includeConfig 'conf/containers.config'
  }
  // Small testing with Singularity profile
  // Singularity images will be pulled automatically
  singularity {
    includeConfig 'conf/base.config'
    includeConfig 'conf/travis.config'
    includeConfig 'conf/genomes.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/genomes.config'
    includeConfig 'conf/singularity-path.config'
  }
  // slurm profile for UPPMAX secure clusters
  // Runs the pipeline using the job scheduler
  // Singularity images are already set up
  slurm {
    includeConfig 'conf/base.config'
    includeConfig 'conf/uppmax-slurm.config'
    includeConfig 'conf/genomes.config'
    includeConfig 'conf/singularity-path.config'
  }
  // Default profile for UPPMAX secure clusters
  // Runs the pipeline locally on a single 16-core node
  // Singularity images are already set up
  standard {
    includeConfig 'conf/base.config'
    includeConfig 'conf/uppmax-localhost.config'
    includeConfig 'conf/genomes.config'
    includeConfig 'conf/singularity-path.config'
  }
}

// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
  if(type == 'memory'){
    try {
      if(obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
        return params.max_memory as nextflow.util.MemoryUnit
      else
        return obj
    } catch (all) {
      println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
      return obj
    }
  } else if(type == 'time'){
    try {
      if(obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
        return params.max_time as nextflow.util.Duration
      else
        return obj
    } catch (all) {
      println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
      return obj
    }
  } else if(type == 'cpus'){
    try {
      return Math.min( obj, params.max_cpus as int )
    } catch (all) {
      println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
      return obj
    }
  }
}