DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.6.3

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

sampleSheet:
  filePath: SampleSheet.csv
  filePathList:
    - inputs/SampleSheet.csv
    - SampleSheet.csv
  dataHeaderRowMarker: 
    - "[TSO500L_Data]"
    - "[Cloud_TSO500L_Data]"

jointFiles:
  msiFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
  tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
  snvFiles: Results/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf
  cnvFiles: Results/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf, Optional
  svFiles:
    - Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.sv.vcf, Optional
    - Logs_Intermediates/DnaFusionFiltering/{sampleId.DNA}/{sampleId.DNA}_Fusions.csv, Optional
  metricsQCFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv

sampleFiles:
  tumorPairId:
    alignmentFiles:
      dnaBamFile: "Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
      dnaBaiFile: "Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"