pipeline:
  type: TSO500
  successMarkerFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
  failureMarkerFile: ./failure.txt

sampleSheet:
  filePath: SampleSheet.csv

jointFiles:
  purityPloidyFiles: Logs_Intermediates/CombinedVariantOutput/{pairId}/{pairId}_CombinedVariantOutput.tsv, Optional
  gisFile: Logs_Intermediates/Gis/{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional
  msiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
  tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
  snvFiles: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional
  cnvFiles:
    - Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional
    - Logs_Intermediates/LrCalculator/{sampleId.DNA}/{sampleId.DNA}_DragenExonCNV.vcf, Optional
  rnaSpliceFiles: Logs_Intermediates/RnaSpliceVariantCalling/{sampleId.RNA}/{sampleId.RNA}_SpliceVariants.vcf, Optional
  rnaFusionFiles:
    - Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional
    - Logs_Intermediates/RnaFusion/{sampleId.RNA}/{sampleId.RNA}_AllFusions.csv, Optional
  metricsQCFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv

sampleFiles:
  tumorPairId:
    visualizationFiles:
      coverageFiles: Logs_Intermediates/DnaDragenExonCnvCaller/{sampleId.DNA}/{sampleId.DNA}.target.counts.gc-corrected.gz, Optional
    alignmentFiles:
      dnaBamFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.bam, Optional
      dnaBaiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.bam.bai, Optional
      rnaBamFile: Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.bam, Optional
      rnaBaiFile: Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional

pipeline:
  type: TSO500
  successMarkerFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
  failureMarkerFile: ./failure.txt

sampleSheet:
  filePath: SampleSheet.csv

jointFiles:
  purityPloidyFiles: Logs_Intermediates/CombinedVariantOutput/{pairId}/{pairId}_CombinedVariantOutput.tsv, Optional
  gisFile: Logs_Intermediates/Gis/{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional
  msiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
  tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
  snvFiles: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional
  cnvFiles:
    - Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional
    - Logs_Intermediates/LrCalculator/{sampleId.DNA}/{sampleId.DNA}_DragenExonCNV.vcf, Optional
  rnaSpliceFiles: Logs_Intermediates/RnaSpliceVariantCalling/{sampleId.RNA}/{sampleId.RNA}_SpliceVariants.vcf, Optional
  rnaFusionFiles:
    - Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional
    - Logs_Intermediates/RnaFusion/{sampleId.RNA}/{sampleId.RNA}_AllFusions.csv, Optional
  metricsQCFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv

sampleFiles:
  tumorPairId:
    visualizationFiles:
      coverageFiles: Logs_Intermediates/DnaDragenExonCnvCaller/{sampleId.DNA}/{sampleId.DNA}.target.counts.gc-corrected.gz, Optional
    alignmentFiles:
      dnaBamFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.bam, Optional
      dnaBaiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.bam.bai, Optional
      rnaBamFile: Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.bam, Optional
      rnaBaiFile: Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional

pipeline:
  type: TSO500
  sampleType: DNA
  successMarkerFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
  failureMarkerFile: ./failure.txt

sampleSheet:
  filePath: SampleSheet.csv

jointFiles:
  msiFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
  tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
  snvFiles: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf
  cnvFiles: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf, Optional
  svFiles: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.sv.vcf, Optional
  metricsQCFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv

sampleFiles:
  tumorPairId:
    alignmentFiles:
      dnaBamFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam
      dnaBaiFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai

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"
  rnaSpliceFiles: "{sampleId.RNA}/{sampleId.RNA}.splice_variants.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"

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"

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"

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"

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

sampleSheet:
  filePath: "SampleSheet.csv"
  
jointFiles:
  purityPloidyFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
    - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
  gisFile:
    - "{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional"
    - "{prefix}/{prefix}.gis.json, Optional"
  msiFile:
    - "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
    - "{prefix}/{prefix}.microsat_output.json, Optional"
  tmbFile:
    - "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
    - "{prefix}/{prefix}.tmb.metrics.csv, Optional"
  snvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
    - "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
  cnvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
    - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
  svFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
    - "{prefix}/{prefix}.sv.vcf.gz, Optional"
  metricsQCFile:
    - "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
    - "{prefix}/{prefix}.mapping_metrics.csv, Optional"
    - "{prefix}/{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
    - "{prefix}/{prefix}.wgs_coverage_metrics_normal.csv, Optional"
    - "{prefix}/{prefix}.vc_metrics.csv, Optional"
    - "{prefix}/{prefix}.cnv_metrics.csv, Optional"
    - "{prefix}/{prefix}.sv_metrics.csv, Optional"

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

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"

pipeline:
  type: TSO500
  sampleType: DNA
  successMarkerFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
  failureMarkerFile: ./failure.txt

sampleSheet:
  filePath: SampleSheet.csv

jointFiles:
  msiFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
  tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
  snvFiles: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf
  cnvFiles: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf, Optional
  svFiles: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.sv.vcf, Optional
  metricsQCFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv

sampleFiles:
  tumorPairId:
    alignmentFiles:
      dnaBamFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam
      dnaBaiFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai

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

sampleSheet:
  filePath: "SampleSheet.csv"
  
jointFiles:
  purityPloidyFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
    - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
  gisFile:
    - "{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional"
    - "{prefix}/{prefix}.gis.json, Optional"
  msiFile:
    - "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
    - "{prefix}/{prefix}.microsat_output.json, Optional"
  tmbFile:
    - "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
    - "{prefix}/{prefix}.tmb.metrics.csv, Optional"
  snvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
    - "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
  cnvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
    - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
  svFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
    - "{prefix}/{prefix}.sv.vcf.gz, Optional"
  metricsQCFile:
    - "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
    - "{prefix}/{prefix}.mapping_metrics.csv, Optional"
    - "{prefix}/{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
    - "{prefix}/{prefix}.wgs_coverage_metrics_normal.csv, Optional"
    - "{prefix}/{prefix}.vc_metrics.csv, Optional"
    - "{prefix}/{prefix}.cnv_metrics.csv, Optional"
    - "{prefix}/{prefix}.sv_metrics.csv, Optional"

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

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

sampleSheet:
  filePath: "SampleSheet.csv"

jointFiles:
  purityPloidyFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
    - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
  gisFile:
    - "{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional"
    - "{prefix}/{prefix}.gis.json, Optional"
  msiFile:
    - "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
    - "{prefix}/{prefix}.microsat_output.json, Optional"
  tmbFile:
    - "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
    - "{prefix}/{prefix}.tmb.metrics.csv, Optional"
  snvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
    - "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
  cnvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
    - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
  svFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
    - "{prefix}/{prefix}.sv.vcf.gz, Optional"
  metricsQCFile:
    - "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
    - "{prefix}/{prefix}.mapping_metrics.csv, Optional"
    - "{prefix}/{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
    - "{prefix}/{prefix}.wgs_coverage_metrics_normal.csv, Optional"
    - "{prefix}/{prefix}.vc_metrics.csv, Optional"
    - "{prefix}/{prefix}.cnv_metrics.csv, Optional"
    - "{prefix}/{prefix}.sv_metrics.csv, Optional"

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

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

jointFiles:
  purityPloidyFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
    - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
  gisFile:
    - "{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional"
    - "{prefix}/{prefix}.gis.json, Optional"
  msiFile:
    - "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
    - "{prefix}/{prefix}.microsat_output.json, Optional"
  tmbFile:
    - "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
    - "{prefix}/{prefix}.tmb.metrics.csv, Optional"
  snvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
    - "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
  cnvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
    - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
  svFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
    - "{prefix}/{prefix}.sv.vcf.gz, Optional"
  metricsQCFile:
    - "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
    - "{prefix}/{prefix}.mapping_metrics.csv, Optional"
    - "{prefix}/{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
    - "{prefix}/{prefix}.wgs_coverage_metrics_normal.csv, Optional"
    - "{prefix}/{prefix}.vc_metrics.csv, Optional"
    - "{prefix}/{prefix}.cnv_metrics.csv, Optional"
    - "{prefix}/{prefix}.sv_metrics.csv, Optional"

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

pipeline:
  successMarkerFile: "Reports/MetricsOutput.tsv"
  failureMarkerFile: "./failure.txt"

sampleSheet:
  filePath: "SampleSheet.csv"
  columnAliases:
    sampleId: Sample_ID
    sampleType: Manifest
    caseId: Pair_ID
    disease:
      id: Tumor_Type
      name: Sample_Description

jointFiles:
  msiFile: "Logs_Intermediates/DNA_IntermediateFiles/MSI/{sampleId.DNA}_MSI.json, Optional"
  snvFiles: "{sampleId.DNA}/{sampleId.DNA}_SmallVariants.genome.vcf, Optional"
  cnvFiles: "{sampleId.DNA}/{sampleId.DNA}_CopyNumberVariants.vcf, Optional"
  rnaSpliceFiles: "Logs_Intermediates/RNA_IntermediateFiles/SpliceVariantCalling/{sampleId.RNA}_SpliceVariants.vcf, Optional"
  rnaFusionFiles: "Logs_Intermediates/RNA_IntermediateFiles/FusionCalling/{sampleId.RNA}_Fusions.csv, Optional"
  metricsQCFile: "Reports/MetricsOutput.tsv"

sampleFiles:
  tumorPairId:
    alignmentFiles:
      dnaBamFile: "Logs_Intermediates/DNA_IntermediateFiles/Alignment/{sampleId.DNA}.bam, Optional"
      dnaBaiFile: "Logs_Intermediates/DNA_IntermediateFiles/Alignment/{sampleId.DNA}.bam.bai, Optional"
      rnaBamFile: "Logs_Intermediates/RNA_IntermediateFiles/Alignment/{sampleId.RNA}.bam, Optional"
      rnaBaiFile: "Logs_Intermediates/RNA_IntermediateFiles/Alignment/{sampleId.RNA}.bam.bai, Optional"

pipeline:
  type: TSO500
  sampleType: DNA
  successMarkerFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
  failureMarkerFile: ./failure.txt

sampleSheet:
  filePath: SampleSheet.csv

jointFiles:
  msiFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
  tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
  snvFiles: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf
  cnvFiles: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf, Optional
  svFiles: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.sv.vcf, Optional
  metricsQCFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv

sampleFiles:
  tumorPairId:
    alignmentFiles:
      dnaBamFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam
      dnaBaiFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai

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

sampleSheet:
  filePath: "SampleSheet.csv"

jointFiles:
  purityPloidyFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
    - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
  gisFile:
    - "{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional"
    - "{prefix}/{prefix}.gis.json, Optional"
  msiFile:
    - "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
    - "{prefix}/{prefix}.microsat_output.json, Optional"
  tmbFile:
    - "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
    - "{prefix}/{prefix}.tmb.metrics.csv, Optional"
  snvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
    - "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
  cnvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
    - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
  svFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
    - "{prefix}/{prefix}.sv.vcf.gz, Optional"
  metricsQCFile:
    - "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
    - "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
    - "{prefix}/{prefix}.mapping_metrics.csv, Optional"
    - "{prefix}/{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
    - "{prefix}/{prefix}.wgs_coverage_metrics_normal.csv, Optional"
    - "{prefix}/{prefix}.vc_metrics.csv, Optional"
    - "{prefix}/{prefix}.cnv_metrics.csv, Optional"
    - "{prefix}/{prefix}.sv_metrics.csv, Optional"

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

pipeline:
  sampleType: DNA
  successMarkerFile: "Analysis_Summary/SampleMetricsReport.txt"
  failureMarkerFile: "./failure.txt"

sampleSheet:
  filePath: "SampleSheet.csv"

jointFiles:
  snvFiles:
    - "{sampleId.DNA}/{sampleId.DNA}.sample.genome.vcf, Optional"
  svFiles: "{sampleId.DNA}/{sampleId.DNA}_Amplifications.vcf, Optional"

sampleFiles:
  tumorPairId:
    alignmentFiles:
      dnaBamFile: "{sampleId.DNA}/MergedBam/{sampleId.DNA}.bam, Optional"
      dnaBaiFile: "{sampleId.DNA}/MergedBam/{sampleId.DNA}.bam.bai, Optional"