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Metrics.wdl 2.1KB

1 year ago
1 year ago
1 year ago
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  1. task Metrics {
  2. File ref_dir
  3. String SENTIEON_INSTALL_DIR
  4. String sample
  5. String docker
  6. String cluster_config
  7. String fasta
  8. File sorted_bam
  9. File sorted_bam_index
  10. String disk_size
  11. command <<<
  12. set -o pipefail
  13. set -e
  14. export SENTIEON_LICENSE=192.168.0.55:8990
  15. nt=$(nproc)
  16. ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${sorted_bam} --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 CoverageMetrics --omit_base_output ${sample}_coverage_metrics
  17. ${SENTIEON_INSTALL_DIR}/bin/sentieon plot metrics -o ${sample}_metrics_report.pdf gc=${sample}_gc_metrics.txt qd=${sample}_qd_metrics.txt mq=${sample}_mq_metrics.txt isize=${sample}_is_metrics.txt
  18. >>>
  19. runtime {
  20. docker:docker
  21. cluster: cluster_config
  22. systemDisk: "cloud_ssd 40"
  23. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  24. }
  25. output {
  26. File qd_metrics = "${sample}_qd_metrics.txt"
  27. File qd_metrics_pdf = "${sample}_qd_metrics.pdf"
  28. File mq_metrics = "${sample}_mq_metrics.txt"
  29. File mq_metrics_pdf = "${sample}_mq_metrics.pdf"
  30. File is_metrics = "${sample}_is_metrics.txt"
  31. File is_metrics_pdf = "${sample}_is_metrics.pdf"
  32. File gc_summary = "${sample}_gc_summary.txt"
  33. File gc_metrics = "${sample}_gc_metrics.txt"
  34. File gc_metrics_pdf = "${sample}_gc_metrics.pdf"
  35. File aln_metrics = "${sample}_aln_metrics.txt"
  36. File coverage_metrics_sample_summary = "${sample}_coverage_metrics.sample_summary"
  37. File coverage_metrics_sample_statistics = "${sample}_coverage_metrics.sample_statistics"
  38. File coverage_metrics_sample_interval_statistics = "${sample}_coverage_metrics.sample_interval_statistics"
  39. File coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_coverage_metrics.sample_cumulative_coverage_proportions"
  40. File coverage_metrics_sample_cumulative_coverage_counts = "${sample}_coverage_metrics.sample_cumulative_coverage_counts"
  41. }
  42. }