# Pillar Biosciences RUO PiVAT Pipeline v2024

```
pipeline:
  successMarkerFile: "pivat_complete.ini"
  failureMarkerFile: "failure.txt"

sampleSheet:
  #required
  filePath: "output_manifest_(.*).ini"
  #optional
  dataHeaderRowMarker: "[PiVAT_Data]"
  #optional
  columnAliases:
    sampleId: Sample_ID
    sex: Sex
    caseId: Pair_ID
    disease:
      id: Tumor_Type

jointFiles:
  snvFiles:
    - "system/final_report_(.*)/{sampleId.DNA}/{sampleId.DNA}_PiVAT_FINAL_REPORT_VCF_RESULTS_(.*).vcf"
  cnvFiles:
    - "system/final_report_(.*)/{sampleId.DNA}/{sampleId.DNA}_PiVAT_FINAL_REPORT_CNV_VCF_RESULTS_(.*).vcf, Optional"
  rnaFusionFiles:
    - "system/final_report_(.*)/{sampleId.RNA}/{sampleId.RNA}_PiVAT_FINAL_REPORT_STAR_FUSION_VCF_RESULTS_(.*).vcf"
  msiFile:
    - "system/MSI_RESULTS_(.*).p, Optional"
  metricsQCFile:
    - "system/{sampleId.DNA}_PiVATSAMPLE_TRANSFER_FILE_(.*).p, Optional"
    - "system/{sampleId.RNA}_PiVATSTAR_FUSION_SAMPLE_TRANSFER_FILE_(.*).p, Optional"
    - "system/TRANSFER_FILE_(.*).p, Optional"

sampleFiles:
  tumorPairId:
    alignmentFiles:
      dnaBamFile:
        - "{sampleId.DNA}/analysis/{sampleId.DNA}_PiVATBAM_(.*).bam, Optional"
      dnaBaiFile:
        - "{sampleId.DNA}/analysis/{sampleId.DNA}_PiVATBAM_(.*).bam.bai, Optional"
      rnaBamFile:
        - "{sampleId.RNA}/analysis/{sampleId.RNA}_PiVATSBAM_(.*).bam, Optional"
      rnaBaiFile:
        - "{sampleId.RNA}/analysis/{sampleId.RNA}_PiVATSBAM_(.*).bam.bai, Optional"
```


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