DRAGEN Heme v1.0

pipeline:
  sampleType: DNA
  successMarkerFile: "Results/MetricsOutput.tsv"
  failureMarkerFile: "./failure.txt"

sampleSheet:
  filePath: "SampleSheet.csv"
  dataHeaderRowMarker: "[Heme_Data]"

jointFiles:
  purityPloidyFiles: "Results/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
  snvFiles: "Results/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz"
  cnvFiles: "Results/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
  svFiles: "Results/{sampleId.DNA}/{sampleId.DNA}.sv.small_indel_dedup.filtered.vcf.gz, Optional"
  metricsQCFile: "Results/MetricsOutput.tsv, Optional"

sampleFiles:
  tumorPairId:
    visualizationFiles:
      coverageFiles: "Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
      ballelesFiles: "Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
    alignmentFiles:
      dnaBamFile: "Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
      dnaBaiFile: "Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"

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