DRAGEN for Illumina cfDNA Prep with Enrichment v4.0.3

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"

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

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"
      ballelesFiles:
        - "{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
        - "{prefix}.tumor.baf.bedgraph.gz, Optional"
        - "{prefix}/{prefix}.tumor.baf.bedgraph.gz, Optional"
        - "{sampleId.DNA}/{sampleId.DNA}.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"