DRAGEN RNA v4.3

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

sampleSheet:
  filePath: SampleSheet.csv

jointFiles:
  snvFiles:
    - "{sampleId.RNA}/{sampleId.RNA}.hard-filtered.vcf.gz, Optional"
    - "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
    - "{prefix}.hard-filtered.vcf.gz, Optional"
    - "{sampleId.RNA}.hard-filtered.vcf.gz, Optional"
  rnaGeneExpressionFiles:
    - "{sampleId.RNA}/{sampleId.RNA}.quant.genes.sf, Optional"
    - "{prefix}/{prefix}.quant.genes.sf, Optional"
    - "{sampleId.RNA}.quant.genes.sf, Optional"
    - "{prefix}.quant.genes.sf, Optional"
  rnaFusionFiles:
    - "{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
    - "{prefix}/{prefix}.fusion_candidates.vcf.gz, Optional"
    - "{prefix}.fusion_candidates.vcf.gz, Optional"
    - "{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
  rnaSpliceFiles:
    - "{sampleId.RNA}/{sampleId.RNA}.splice_variants.vcf.gz, Optional"
    - "{sampleId.RNA}.splice_variants.vcf.gz, Optional"
    - "{prefix}/{prefix}.splice_variants.vcf.gz, Optional"
    - "{prefix}.splice_variants.vcf.gz, Optional"
  metricsQCFile:
    - "{sampleId.RNA}/{sampleId.RNA}.mapping_metrics.csv, Optional"
    - "{prefix}/{prefix}.mapping_metrics.csv, Optional"
    - "{prefix}.mapping_metrics.csv, Optional"
    - "{sampleId.RNA}.mapping_metrics.csv, Optional"

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