PoN/tasks/PoN.wdl

task PoN {

  String SENTIEON_INSTALL_DIR
  String SENTIEON_LICENSE
  File ref_dir
  String fasta
  File cosmic_dir
  String cosmic_vcf
  File dbsnp_dir
  String dbsnp
  File regions

  File normal_bam
  File normal_bam_index
  String sample=basename(normal_bam, ".*")
  String docker
  String cluster_config
  String disk_size
  
  command <<<
    set -o pipefail
    set -e
    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
    nt=$(nproc)
    mkdir -p /cromwell_root/tmp/cosmic/
    cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/cosmic/
    ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/cosmic/${cosmic_vcf}

    # Generating TNhaplotyper PoN
    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNhaplotyper --detect_pon --cosmic /cromwell_root/tmp/cosmic/${cosmic_vcf} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}_TNhaplotyper_pon.vcf

    # Generating TNhaplotyper2 PoN
    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNhaplotyper2 --normal_sample ${sample} ${sample}_TNhaplotyper2_pon.vcf

    # Generating TNscope PoN
    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNscope --normal_sample ${sample} ${sample}_TNscope_pon.vcf
  >>>
  
  runtime {
    docker: docker
    cluster: cluster_config
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"  
  }

  output {
    File TNhaplotyper_pon_vcf = "${sample}_TNhaplotyper_pon.vcf"
    File TNhaplotyper2_pon_vcf = "${sample}_TNhaplotyper2_pon.vcf"
    File TNscope_pon_vcf = "${sample}_TNscope_pon.vcf"
  }
}