nextflow.config

// config for Parapipe processes

profiles {
  singularity {

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

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

    process {

      withName:getRefData {
        container = "${params.sif_dir}/preprocessing.sif"
      }

      withName:indexRefData {
        container = "${params.sif_dir}/preprocessing.sif"
      }

      withName:checkFqValidity {
        container = "${params.sif_dir}/preprocessing.sif"
      }

      withName:countReads {
        container = "${params.sif_dir}/preprocessing.sif"
      }

      withName:fastp {
        container = "${params.sif_dir}/preprocessing.sif"
      }

      withName:fastQC {
        container = "${params.sif_dir}/preprocessing.sif"
      }

      withName:multiQC {
        container = "${params.sif_dir}/preprocessing.sif"
      }

      withName:trimGalore {
        container = "${params.sif_dir}/preprocessing.sif"
      }

      withName:map2Ref {
        container = "${params.sif_dir}/preprocessing.sif"
      }

      withName:picard {
        container = "${params.sif_dir}/preprocessing.sif"
      }

      withName:summarise {
        container = "${params.sif_dir}/preprocessing.sif"
      }

      withName:callVariants {
        container = "${params.sif_dir}/parapipe.sif"
      }

      withName:moi {
        container = "${params.sif_dir}/moi.sif"
      }

      withName:formatPhyloInput {
        container = "${params.sif_dir}/parapipe.sif"
      }

      withName:molTyping_phylo {
        container = "${params.sif_dir}/parapipe.sif"
      }

      withName:wgSNV_phylo {
        container = "${params.sif_dir}/parapipe.sif"
      }

      withName:makeJSON {
        container = "${params.sif_dir}/parapipe.sif"
      }

      withName:makeSampleReports {
        container = "${params.sif_dir}/parapipe.sif"
      }

      withName:makeRunReport {
        container = "${params.sif_dir}/parapipe.sif"
      }
    }
  }
}