pipeline:
type: TSO500
sampleType: DNA
successMarkerFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
failureMarkerFile: ./failure.txt
sampleSheet:
filePath: SampleSheet.csv
jointFiles:
msiFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
snvFiles: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf
cnvFiles: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf, Optional
svFiles:
- Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}.sv.vcf, Optional
- Logs_Intermediates/DnaFusionFiltering/{sampleId.DNA}/{sampleId.DNA}_Fusions.csv, Optional
metricsQCFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
sampleFiles:
tumorPairId:
alignmentFiles:
dnaBamFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam
dnaBaiFile: Logs_Intermediates/DragenCaller/{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai
