DRAGEN Amplicon v4.1

pipeline:
  type: WGS
  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"
    - "{sampleId.RNA}.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, 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"
  rnaFusionFiles:
    - "{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
    - "{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
    - "{prefix}/{prefix}.fusion_candidates.vcf.gz, Optional"
    - "{prefix}.fusion_candidates.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}.target_bed_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.RNA}/{sampleId.RNA}.mapping_metrics.csv, Optional"
    - "{sampleId.RNA}/{sampleId.RNA}.wgs_coverage_metrics.csv, Optional"
    - "{sampleId.RNA}/{sampleId.RNA}.target_bed_coverage_metrics.csv, Optional"
    - "{sampleId.DNA}.mapping_metrics.csv, Optional"
    - "{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
    - "{sampleId.DNA}.target_bed_coverage_metrics.csv, Optional"
    - "{sampleId.DNA}.vc_metrics.csv, Optional"
    - "{sampleId.DNA}.cnv_metrics.csv, Optional"
    - "{sampleId.DNA}.sv_metrics.csv, Optional"
    - "{sampleId.RNA}.mapping_metrics.csv, Optional"
    - "{sampleId.RNA}.wgs_coverage_metrics.csv, Optional"
    - "{sampleId.RNA}.target_bed_coverage_metrics.csv, Optional"
    - "{prefix}/{prefix}.mapping_metrics.csv, Optional"
    - "{prefix}/{prefix}.wgs_coverage_metrics.csv, Optional"
    - "{prefix}/{prefix}.target_bed_coverage_metrics.csv, Optional"
    - "{prefix}/{prefix}.vc_metrics.csv, Optional"
    - "{prefix}/{prefix}.cnv_metrics.csv, Optional"
    - "{prefix}/{prefix}.sv_metrics.csv, Optional"    
    - "{prefix}.mapping_metrics.csv, Optional"
    - "{prefix}.wgs_coverage_metrics.csv, Optional"
    - "{prefix}.target_bed_coverage_metrics.csv, Optional"
    - "{prefix}.vc_metrics.csv, Optional"
    - "{prefix}.cnv_metrics.csv, Optional"
    - "{prefix}.sv_metrics.csv, Optional"


sampleFiles:
  tumorPairId:
    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"
      rnaBamFile:
        - "{sampleId.RNA}/{sampleId.RNA}_tumor.bam, Optional"
        - "{sampleId.RNA}/{sampleId.RNA}.bam, Optional"
        - "{sampleId.RNA}_tumor.bam, Optional"
        - "{sampleId.RNA}.bam, Optional"
        - "{prefix}_tumor.bam, Optional"
        - "{prefix}.bam, Optional"
      rnaBaiFile:
        - "{sampleId.RNA}/{sampleId.RNA}_tumor.bam.bai, Optional"
        - "{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional"
        - "{sampleId.RNA}_tumor.bam.bai, Optional"
        - "{sampleId.RNA}.bam.bai, Optional"
        - "{prefix}_tumor.bam.bai, Optional"
        - "{prefix}.bam.bai, Optional"