DRAGEN RNA v4.1

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

jointFiles:
  snvFiles: "{sampleId.RNA}/{sampleId.RNA}.hard-filtered.vcf.gz, Optional"
  rnaFusionFiles: "{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
  metricsQCFile:
    - "{sampleId.RNA}/{sampleId.RNA}.mapping_metrics.csv"

sampleFiles:
  tumorPairId:
    alignmentFiles:
      rnaBamFile: "{sampleId.RNA}/{sampleId.RNA}.bam, Optional"
      rnaBaiFile: "{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional"