PoN/tasks/Dedup.wdl

task Dedup {

  String SENTIEON_INSTALL_DIR
  String SENTIEON_LICENSE
  String sample

  File sorted_bam
  File sorted_bam_index
  String docker
  String cluster_config
  String disk_size

  command <<<
    set -o pipefail
    set -e
    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
    nt=$(nproc)
    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo LocusCollector --fun score_info ${sample}_score.txt
    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo Dedup --rmdup --score_info ${sample}_score.txt --metrics ${sample}_dedup_metrics.txt ${sample}.sorted.deduped.bam
  >>>
  
  runtime {
    docker: docker
    cluster: cluster_config
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }

  output {
    File score = "${sample}_score.txt"
    File dedup_metrics = "${sample}_dedup_metrics.txt"
    File deduped_bam = "${sample}.sorted.deduped.bam"
    File deduped_bam_index = "${sample}.sorted.deduped.bam.bai"
  }
}