variant-calling/tasks/Haplotyper.wdl

task Haplotyper {
  
  File ref_dir
  File dbsnp_dir
  
  String SENTIEON_INSTALL_DIR
  String SENTIEON_LICENSE
  String fasta
  File recaled_bam
  File recaled_bam_index
  File recal_table
  String dbsnp
  String sample
  String docker
  String cluster_config
  String disk_size

  File? regions
  Int? interval_padding

  command <<<
    set -o pipefail
    set -e
    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
    nt=$(nproc)

    if [ ${regions} ]; then
      INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
    else
      INTERVAL=""
    fi

    if [ ${pon_vcf} ]; then
      PON="--pon ${pon_vcf}"
      ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${pon_vcf}
    else
      PON=""
    fi

    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
	--interval ${regions} -r ${ref_dir}/${fasta} \
	-i ${recaled_bam} -q ${recal_table}\
	--algo Haplotyper -d ${dbsnp_dir}/${dbsnp} \
	${sample}_hc.vcf
  >>>
  
  runtime {
    docker: docker
    cluster: cluster_config
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }

  output {
    File vcf = "${sample}_hc.vcf"
    File vcf_idx = "${sample}_hc.vcf.idx"
  }
}