WesPipe-hg19-bam/tasks/TNseq.wdl

task TNseq {
  
  String sample
  String SENTIEON_LICENSE
  File tumor_bam
  File tumor_bam_index
  File? normal_bam
  File? normal_bam_index
  String tumor_name
  String normal_name
  
  File ref_dir
  String fasta
  File germline_resource
  File germline_resource_tbi
  File? regions
  Int? interval_padding
  
  String docker
  String cluster_config
  String disk_size

  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 [ ${normal_bam} ]; then
      INPUT="-i ${tumor_bam} -i ${normal_bam}"
      SAMPLE="--tumor_sample ${tumor_name} --normal_sample ${normal_name}"
    else
      INPUT="-i ${tumor_bam}"
      SAMPLE="--tumor_sample ${tumor_name}"
    fi
    
    # sentieon driver -t $nt -r ${ref_dir}/${fasta} \
    # $INPUT $INTERVAL \
    # --algo TNhaplotyper2 $SAMPLE \
    # --germline_vcf ${germline_resource} \
    # ${sample}.TNseq.raw.vcf \
    # --algo OrientationBias --tumor_sample ${tumor_name} \
    # ${sample}.orientation \
    # --algo ContaminationModel $SAMPLE \
    # --vcf ${germline_resource} \
    # --tumor_segments ${sample}.contamination.segments \
    # ${sample}.contamination
    
    # sentieon driver -t $nt \
    # -r ${ref_dir}/${fasta} \
    # --algo TNfilter $SAMPLE \
    # -v ${sample}.TNseq.raw.vcf \
    # --contamination ${sample}.contamination \
    # --tumor_segments ${sample}.contamination.segments \
    # --orientation_priors ${sample}.orientation \
    # ${sample}.TNseq.vcf

    sentieon driver -t $nt -r ${ref_dir}/${fasta} \
    $INPUT $INTERVAL \
    --algo TNhaplotyper2 $SAMPLE \
    ${sample}.TNseq.raw.vcf
    
    sentieon driver -t $nt \
    -r ${ref_dir}/${fasta} \
    --algo TNfilter $SAMPLE \
    -v ${sample}.TNseq.raw.vcf \
    ${sample}.TNseq.vcf

    touch ${sample}.contamination
    touch ${sample}.contamination.segments
    touch ${sample}.orientation
  >>>
  
  runtime {
    docker: docker
    cluster: cluster_config
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }
  
  output {
    File raw_vcf = "${sample}.TNseq.raw.vcf"
    File raw_vcf_index = "${sample}.TNseq.raw.vcf.idx"
    File vcf = "${sample}.TNseq.vcf"
    File vcf_index = "${sample}.TNseq.vcf.idx"
    File contamination = "${sample}.contamination"
    File contamination_segments = "${sample}.contamination.segments"
    File orientation = "${sample}.orientation"
  }
}