DRAGEN Somatic Enrichment and Whole Genome v4.4.6

pipeline:
    type: WGS
    sampleType: DNA
    successMarkerFile: 
      - "{prefix}/{prefix}.time_metrics.csv, Optional"
      - "{prefix}.time_metrics.csv, Optional"
      - "{sampleId.DNA}.time_metrics.csv, Optional"
      - "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"    
    failureMarkerFile: "failure.txt"
  
  sampleSheet:
    filePath: "SampleSheet.csv"
    dataHeaderRowMarker: 
      - "[DragenEnrichment_Data]"
      - "[DragenSomaticEnrichment_Data]"
      - "[Cloud_DragenEnrichment_Data]"  
      - "[Cloud_DragenSomaticEnrichment_Data]"  
  
  jointFiles:
    purityPloidyFiles:
      - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
      - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
      - "{prefix}.cnv.vcf.gz, Optional"
      - "{sampleId.DNA}.cnv.vcf.gz, Optional"
    hrdFile:
      - "{sampleId.DNA}/{sampleId.DNA}.hrdscore.csv, Optional"
      - "{prefix}/{prefix}.hrdscore.csv, Optional"
      - "{prefix}.hrdscore.csv, Optional"
      - "{sampleId.DNA}.hrdscore.csv, Optional"
    hlaFile:
      - "{sampleId.DNA}/{sampleId.DNA}.hla.tsv, Optional"
      - "{prefix}/{prefix}.hla.tsv, Optional"
      - "{prefix}.hla.tsv, Optional"
      - "{sampleId.DNA}.hla.tsv, Optional"
    msiFile:
      - "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
      - "{prefix}/{prefix}.microsat_output.json, Optional"
      - "{prefix}.microsat_output.json, Optional"
      - "{sampleId.DNA}.microsat_output.json, Optional"
    tmbFile:
      - "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
      - "{prefix}/{prefix}.tmb.metrics.csv, Optional"
      - "{prefix}.tmb.metrics.csv, Optional"
      - "{sampleId.DNA}.tmb.metrics.csv, Optional"
    snvFiles:
      - "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
      - "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
      - "{prefix}.hard-filtered.vcf.gz, Optional"
      - "{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
    cnvFiles:
      - "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
      - "{prefix}/{prefix}.cnv.vcf.gz, Optional"
      - "{prefix}.cnv.vcf.gz, Optional"
      - "{sampleId.DNA}.cnv.vcf.gz, Optional"
    svFiles:
      - "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
      - "{sampleId.DNA}/{sampleId.DNA}_Fusions.csv, Optional"
      - "{prefix}/{prefix}.sv.vcf.gz, Optional"
      - "{prefix}/{prefix}_Fusions.csv, Optional"
      - "{prefix}.sv.vcf.gz, Optional"
      - "{prefix}_Fusions.csv, Optional"
      - "{sampleId.DNA}.sv.vcf.gz, Optional"
      - "{sampleId.DNA}_Fusions.csv, Optional"
    metricsQCFile:
      - "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
      - "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
      - "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_normal.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"
      - "{sampleId.DNA}/{sampleId.DNA}.target_bed_coverage_metrics.csv, Optional"
      - "{sampleId.DNA}/{sampleId.DNA}.target_bed_coverage_metrics_normal.csv, Optional"
      - "{sampleId.DNA}/{sampleId.DNA}.target_bed_coverage_metrics_tumor.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}.wgs_coverage_metrics.csv, Optional"
      - "{prefix}/{prefix}.vc_metrics.csv, Optional"
      - "{prefix}/{prefix}.cnv_metrics.csv, Optional"
      - "{prefix}/{prefix}.sv_metrics.csv, Optional"
      - "{prefix}/{prefix}.target_bed_coverage_metrics.csv, Optional"
      - "{prefix}/{prefix}.target_bed_coverage_metrics_normal.csv, Optional"
      - "{prefix}/{prefix}.target_bed_coverage_metrics_tumor.csv, Optional"
      - "{prefix}.mapping_metrics.csv, Optional"
      - "{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
      - "{prefix}.wgs_coverage_metrics_normal.csv, Optional"
      - "{prefix}.wgs_coverage_metrics.csv, Optional"
      - "{prefix}.vc_metrics.csv, Optional"
      - "{prefix}.cnv_metrics.csv, Optional"
      - "{prefix}.sv_metrics.csv, Optional"
      - "{prefix}.target_bed_coverage_metrics.csv, Optional"
      - "{prefix}.target_bed_coverage_metrics_normal.csv, Optional"
      - "{prefix}.target_bed_coverage_metrics_tumor.csv, Optional"
      - "{sampleId.DNA}.mapping_metrics.csv, Optional"
      - "{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
      - "{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
      - "{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
      - "{sampleId.DNA}.vc_metrics.csv, Optional"
      - "{sampleId.DNA}.cnv_metrics.csv, Optional"
      - "{sampleId.DNA}.sv_metrics.csv, Optional"
      - "{sampleId.DNA}.target_bed_coverage_metrics.csv, Optional"
      - "{sampleId.DNA}.target_bed_coverage_metrics_normal.csv, Optional"
      - "{sampleId.DNA}.target_bed_coverage_metrics_tumor.csv, Optional"
  
  
  sampleFiles:
    tumorPairId:
      visualizationFiles:
        coverageFiles:
          - "{sampleId.DNA}/{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
          - "{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
          - "{prefix}/{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
          - "{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
        coverageBedFiles:
          - "{sampleId.DNA}.target_bed_read_cov_report.bed, Optional"
          - "{sampleId.DNA}/{sampleId.DNA}.target_bed_read_cov_report.bed, Optional"
          - "{prefix}.target_bed_read_cov_report.bed, Optional"
          - "{prefix}/{prefix}.target_bed_read_cov_report.bed, Optional"
          - "{sampleId.DNA}/{sampleId.DNA}.target_bed_read_cov_report_tumor.bed, Optional"
          - "{sampleId.DNA}.target_bed_read_cov_report_tumor.bed, Optional"
          - "{prefix}/{prefix}.target_bed_read_cov_report_tumor.bed, Optional"
          - "{prefix}.target_bed_read_cov_report_tumor.bed, Optional"
        ballelesFiles:
          - "{sampleId.DNA}/{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
          - "{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
          - "{prefix}/{prefix}.tumor.baf.bedgraph.gz, Optional"
          - "{prefix}.tumor.baf.bedgraph.gz, Optional"
      alignmentFiles:
        dnaBamFile:
          - "{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
          - "{sampleId.DNA}_tumor.bam, Optional"
          - "{prefix}/{prefix}_tumor.bam, Optional"
          - "{prefix}_tumor.bam, Optional"
        dnaBaiFile:
          - "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
          - "{sampleId.DNA}_tumor.bam.bai, Optional"
          - "{prefix}/{prefix}_tumor.bam.bai, Optional"
          - "{prefix}_tumor.bam.bai, Optional"