DRAGEN Solid WGS Tumor Normal v4.4

pipeline:
  type: WGS
  sampleType: DNA
  successMarkerFile: "SampleSheet.csv"
  failureMarkerFile: "failure.txt"

sampleSheet:
  filePath: "SampleSheet.csv"
  #optional
  dataHeaderRowMarker: "[TN_Data]"
  #optional
  columnAliases:
    sampleId: Sample_ID
    caseId: Case_ID

jointFiles:
  purityPloidyFiles:
    - "Results/{prefix}/{sampleId.tumor.DNA}/{sampleId.tumor.DNA}.cnv.vcf.gz, Optional"
  hrdFile:
    - "Results/{prefix}/{sampleId.tumor.DNA}/{sampleId.tumor.DNA}.hrdscore.csv, Optional"
  msiFile:
    - "Results/{prefix}/{sampleId.tumor.DNA}/{sampleId.tumor.DNA}.microsat_output.json, Optional"
  tmbFile:
    - "Results/{prefix}/{sampleId.tumor.DNA}/{sampleId.tumor.DNA}.tmb.metrics.csv, Optional"
  snvFiles:
    - "Results/{prefix}/{sampleId.tumor.DNA}/{sampleId.tumor.DNA}.hard-filtered.vcf.gz, Optional"
    - "Results/{prefix}/{sampleId.normal.DNA}/{sampleId.normal.DNA}.hard-filtered.vcf.gz, Optional"
  cnvFiles:
    - "Results/{prefix}/{sampleId.tumor.DNA}/{sampleId.tumor.DNA}.cnv.vcf.gz, Optional"
  svFiles:
    - "Results/{prefix}/{sampleId.tumor.DNA}/{sampleId.tumor.DNA}.sv.vcf.gz, Optional"
    - "Results/{prefix}/{sampleId.normal.DNA}/{sampleId.normal.DNA}.sv.vcf.gz, Optional"
  metricsQCFile:
    - "Results/MetricsOutput.tsv"

sampleFiles:
  tumorPairId:
    visualizationFiles:
      coverageFiles:
        - "Logs_Intermediates/TumorNormalVariantCaller/{sampleId.tumor.DNA}/{sampleId.tumor.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
      ballelesFiles:
        - "Results/{prefix}/{sampleId.tumor.DNA}/{sampleId.tumor.DNA}.tumor.baf.bedgraph.gz, Optional"
    alignmentFiles:
      dnaBamFile:
        - "Results/{prefix}/{sampleId.tumor.DNA}/{sampleId.tumor.DNA}.bam, Optional"
      dnaBaiFile:
        - "Results/{prefix}/{sampleId.tumor.DNA}/{sampleId.tumor.DNA}.bam.bai, Optional"
  normalPairId:
    alignmentFiles:
      dnaBamFile:
        - "Results/{prefix}/{sampleId.normal.DNA}/{sampleId.normal.DNA}.bam, Optional"
      dnaBaiFile:
        - "Results/{prefix}/{sampleId.normal.DNA}/{sampleId.normal.DNA}.bam.bai, Optional"