WesPipe/tasks/Metrics.wdl

task Metrics {

  File ref_dir
  String SENTIEON_LICENSE
  String sample
  String docker
  String cluster_config

  String fasta
  File sorted_bam
  File sorted_bam_index
  String disk_size

  File? regions

  command <<<
    set -o pipefail
    set -e
    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
    nt=$(nproc)
    
    if [ ${regions} ]; then
      INTERVAL="--interval ${regions}"
    else
      INTERVAL=""
    fi
    
    sentieon driver -t $nt \
    -r ${ref_dir}/${fasta} $INTERVAL \
    -i ${sorted_bam} \
    --algo CoverageMetrics --omit_base_output ${sample}_coverage_metrics \
    --algo MeanQualityByCycle ${sample}_mq_metrics.txt \
    --algo QualDistribution ${sample}_qd_metrics.txt \
    --algo GCBias --summary ${sample}_gc_summary.txt ${sample}_gc_metrics.txt \
    --algo AlignmentStat ${sample}_aln_metrics.txt \
    --algo InsertSizeMetricAlgo ${sample}_is_metrics.txt \
    --algo QualityYield ${sample}_QualityYield.txt \
    --algo WgsMetricsAlgo ${sample}_WgsMetricsAlgo.txt
    
    sentieon plot metrics -o ${sample}_metrics_report.pdf gc=${sample}_gc_metrics.txt qd=${sample}_qd_metrics.txt mq=${sample}_mq_metrics.txt isize=${sample}_is_metrics.txt
  >>>
  
  runtime {
    docker: docker
    cluster: cluster_config
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }

  output {
    File coverage_metrics_sample_summary = "${sample}_coverage_metrics.sample_summary"
    File coverage_metrics_sample_statistics = "${sample}_coverage_metrics.sample_statistics"
    File coverage_metrics_sample_interval_statistics = "${sample}_coverage_metrics.sample_interval_statistics"
    File coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_coverage_metrics.sample_cumulative_coverage_proportions"
    File coverage_metrics_sample_cumulative_coverage_counts = "${sample}_coverage_metrics.sample_cumulative_coverage_counts"
    File qd_metrics = "${sample}_qd_metrics.txt"
    File mq_metrics = "${sample}_mq_metrics.txt"
    File is_metrics = "${sample}_is_metrics.txt"
    File gc_summary = "${sample}_gc_summary.txt"
    File gc_metrics = "${sample}_gc_metrics.txt"
    File aln_metrics = "${sample}_aln_metrics.txt"
    File QualityYield = "${sample}_QualityYield.txt"
    File wgsmetrics = "${sample}_WgsMetricsAlgo.txt"
    File qd_metrics_pdf = "${sample}_qd_metrics.pdf"
    File mq_metrics_pdf = "${sample}_mq_metrics.pdf"
    File is_metrics_pdf = "${sample}_is_metrics.pdf"
    File gc_metrics_pdf = "${sample}_gc_metrics.pdf"
  }
}