DRAGEN TruSight Oncology 500 Analysis Software v2.1.1 (with HRD)

pipeline:
  type: TSO500
  successMarkerFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
  failureMarkerFile: ./failure.txt

sampleSheet:
  filePath: SampleSheet.csv
  filePathList:
    - inputs/SampleSheet.csv
    - SampleSheet.csv
  dataHeaderRowMarker: 
    - "[TSO500S_Data]"
    - "[Cloud_TSO500S_Data]"

jointFiles:
  purityPloidyFiles: Logs_Intermediates/CombinedVariantOutput/{pairId}/{pairId}_CombinedVariantOutput.tsv, Optional
  gisFile: Logs_Intermediates/Gis/{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional
  msiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
  tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
  snvFiles: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional
  cnvFiles:
    - Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional
    - Logs_Intermediates/LrCalculator/{sampleId.DNA}/{sampleId.DNA}_DragenExonCNV.vcf, Optional
  rnaSpliceFiles: Logs_Intermediates/RnaSpliceVariantCalling/{sampleId.RNA}/{sampleId.RNA}_SpliceVariants.vcf, Optional
  rnaFusionFiles:
    - Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional
    - Logs_Intermediates/RnaFusion/{sampleId.RNA}/{sampleId.RNA}_AllFusions.csv, Optional
  metricsQCFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv

sampleFiles:
  tumorPairId:
    visualizationFiles:
      coverageFiles: Logs_Intermediates/DnaDragenExonCnvCaller/{sampleId.DNA}/{sampleId.DNA}.target.counts.gc-corrected.gz, Optional
    alignmentFiles:
      dnaBamFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.bam, Optional
      dnaBaiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.bam.bai, Optional
      rnaBamFile: Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.bam, Optional
      rnaBaiFile: Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional