nextflow.config

// config for autoDatabase

// define global parameters
params {

  // path to new fasta to be added to database
  addFasta = ""

  // path to fasta from previous database build
  previousDatabase = null

  // path where the new database and other results will be saved
  newDatabase = "${baseDir}/result"

  // date of NCBI taxonomy to download, format YYYY-MM-DD
  ncbiDate = '2020-05-01'

  // range to take around the mode of the average mash distance, default is 10%
  modeRange = '0.1'
}

// define docker and singularity profiles
profiles {
  singularity {

    singularity.enabled = 'true'
    singularity.autoMounts = 'true'

    // path to the singularity containers
    params.sifDir = "${baseDir}/singularity"

    // define containers for each process
    process {
   
      withName:autoDatabase_addTaxon {
        container = "${params.sifDir}/autoDatabase_pythonenv.sif"
      }
  
      withName:autoDatabase_mash {
        container = "${params.sifDir}/autoDatabase_mash.sif"
      }

      withName:autoDatabase_qc {
        container = "${params.sifDir}/autoDatabase_pythonenv.sif"
      }

      withName:autoDatabase_kraken2Build {
        container = "${params.sifDir}/autoDatabase_kraken2.sif"
      }
      withName:autoDatabase_krona {
        container = "${params.sifDir}/autoDatabase_krona.sif"
      }
    }
  }

  docker {
    
    docker.enabled = true
    fixOwnership = true
    runOptions = "-u \$(id -u):\$(id -g)"

    // define containers for each process
    process {
    
      withName:autoDatabase_addTaxon {
        container = "autodatabasepythonenv:latest"
      }
    
      withName:autoDatabase_mash {
        container = "autodatabasemash:latest"
      }

      withName:autoDatabase_qc {
        container = "autodatabasepythonenv:latest"
      }

      withName:autoDatabase_kraken2Build {
        container = "autodatabasekraken2:latest"
      }
      withName:autoDatabase_krona {
        container = "autodatabasekrona:latest"
      }
    } 
  }
}