TruSight Tumor 170 Local App v2.0.1

pipeline:
  successMarkerFile: "Reports/MetricsOutput.tsv"
  failureMarkerFile: "./failure.txt"

sampleSheet:
  filePath: "SampleSheet.csv"
  columnAliases:
    sampleId: Sample_ID
    sampleType: Manifest
    caseId: Pair_ID
    disease:
      id: Tumor_Type
      name: Sample_Description

jointFiles:
  msiFile: "Logs_Intermediates/DNA_IntermediateFiles/MSI/{sampleId.DNA}_MSI.json, Optional"
  snvFiles: "{sampleId.DNA}/{sampleId.DNA}_SmallVariants.genome.vcf, Optional"
  cnvFiles: "{sampleId.DNA}/{sampleId.DNA}_CopyNumberVariants.vcf, Optional"
  rnaSpliceFiles: "Logs_Intermediates/RNA_IntermediateFiles/SpliceVariantCalling/{sampleId.RNA}_SpliceVariants.vcf, Optional"
  rnaFusionFiles: "Logs_Intermediates/RNA_IntermediateFiles/FusionCalling/{sampleId.RNA}_Fusions.csv, Optional"
  metricsQCFile: "Reports/MetricsOutput.tsv"

sampleFiles:
  tumorPairId:
    alignmentFiles:
      dnaBamFile: "Logs_Intermediates/DNA_IntermediateFiles/Alignment/{sampleId.DNA}.bam, Optional"
      dnaBaiFile: "Logs_Intermediates/DNA_IntermediateFiles/Alignment/{sampleId.DNA}.bam.bai, Optional"
      rnaBamFile: "Logs_Intermediates/RNA_IntermediateFiles/Alignment/{sampleId.RNA}.bam, Optional"
      rnaBaiFile: "Logs_Intermediates/RNA_IntermediateFiles/Alignment/{sampleId.RNA}.bam.bai, Optional"