PoN/tasks/mapping.wdl

task mapping {

  File ref_dir
  String fasta
  File fastq_1
  File fastq_2

  String SENTIEON_INSTALL_DIR
  String SENTIEON_LICENSE
  String group
  String sample
  String pl
  String docker
  String cluster_config
  String disk_size

  command <<<
    set -o pipefail
    set -e  
    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
    nt=$(nproc)
    ${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${sample}.sorted.bam -t $nt --sam2bam -i -
  >>>

  runtime {
    docker: docker
    cluster: cluster_config
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }
  output {
    File sorted_bam = "${sample}.sorted.bam"
    File sorted_bam_index = "${sample}.sorted.bam.bai"
  }
}