Archer VariantPlex Pipeline v7.3
pipeline:
successMarkerFile: "SampleSheet.csv"
failureMarkerFile: "failure.txt"
sampleSheet:
filePath: "SampleSheet.csv"
dataHeaderRowMarker: "[Archer_Data]"
jointFiles:
msiFile:
- "{sampleId.DNA}/MSI/loci_results/{sampleId.DNA}_loci_results.tsv, Optional"
snvFiles:
- "{sampleId.DNA}/VCFs/{sampleId.DNA}.combined.filtered.vcf.gz, Optional"
cnvFiles:
- "{sampleId.DNA}/VCFs/{sampleId.DNA}.sv.combined.vcf.gz, Optional"
- "{sampleId.DNA}/VCFs/{sampleId.DNA}.cnv.vcf, Optional"
svFiles:
- "{sampleId.DNA}/VCFs/{sampleId.DNA}.sv.combined.vcf.gz, Optional"
- "{sampleId.DNA}/VCFs/{sampleId.DNA}.sv.vcf, Optional"
sampleFiles:
tumorPairId:
alignmentFiles:
dnaBamFile:
- "{sampleId.DNA}/{sampleId.DNA}.molbar.trimmed.deduped.merged.bam, Optional"
dnaBaiFile:
- "{sampleId.DNA}/{sampleId.DNA}.molbar.trimmed.deduped.merged.bam.bai, Optional"
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