Archer VariantPlex Pipeline v7.3

pipeline:
  successMarkerFile: "SampleSheet.csv"
  failureMarkerFile: "failure.txt"
sampleSheet:
  filePath: "SampleSheet.csv"
  dataHeaderRowMarker: "[Archer_Data]"
jointFiles:
  msiFile:
    - "{sampleId.DNA}/MSI/loci_results/{sampleId.DNA}_loci_results.tsv, Optional"
  snvFiles:
    - "{sampleId.DNA}/VCFs/{sampleId.DNA}.combined.filtered.vcf.gz, Optional"
  cnvFiles:
    - "{sampleId.DNA}/VCFs/{sampleId.DNA}.sv.combined.vcf.gz, Optional"
    - "{sampleId.DNA}/VCFs/{sampleId.DNA}.cnv.vcf, Optional"
  svFiles:
    - "{sampleId.DNA}/VCFs/{sampleId.DNA}.sv.combined.vcf.gz, Optional"
    - "{sampleId.DNA}/VCFs/{sampleId.DNA}.sv.vcf, Optional"
sampleFiles:
  tumorPairId:
    alignmentFiles:
      dnaBamFile:
        - "{sampleId.DNA}/{sampleId.DNA}.molbar.trimmed.deduped.merged.bam, Optional"
      dnaBaiFile:
        - "{sampleId.DNA}/{sampleId.DNA}.molbar.trimmed.deduped.merged.bam.bai, Optional"

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