DRAGEN Amplicon v4.1

pipeline:
  successMarkerFile:
    - "{prefix}/{prefix}.time_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"
    - "{sampleId.RNA}/{sampleId.RNA}.time_metrics.csv, Optional"
  failureMarkerFile: "./failure.txt"

sampleSheet:
  filePath: SampleSheet.csv
  columnAliases:
    sampleType: DnaOrRna
    sampleId: Sample_ID
    pairId: PairID

jointFiles:
  snvFiles: "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz"
  cnvFiles: "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
  svFiles: "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
  rnaFusionFiles: "{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz"
  metricsQCFile:
    - "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv"
    - "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv"
    - "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
    - "{sampleId.RNA}/{sampleId.RNA}.mapping_metrics.csv"
    - "{sampleId.RNA}/{sampleId.RNA}.wgs_coverage_metrics.csv"

sampleFiles:
  tumorPairId:
    alignmentFiles:
      dnaBamFile: "{sampleId.DNA}/{sampleId.DNA}_tumor.bam"
      dnaBaiFile: "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai"
      rnaBamFile: "{sampleId.RNA}/{sampleId.RNA}.bam"
      rnaBaiFile: "{sampleId.RNA}/{sampleId.RNA}.bam.bai"