PoN/tasks/mergePoN.wdl

task mergePoN {

  Array[File] pon_vcfs
  String panel_id
  String docker
  String cluster_config
  String disk_size

  command <<<
    set -o pipefail
    set -e
    mkdir -p /cromwell_root/tmp/bcftools

    for i in ${sep=" " pon_vcfs}
    do
      bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz)
      bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f
    done

    bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > ${panel_id}_pon.vcf
  >>>

  runtime {
    docker: docker
    cluster: cluster_config
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }
  
  output {
    File panel_of_normal_vcf = "${panel_id}_pon.vcf"
  }
}