pipeline:
sampleType: DNA
successMarkerFile: "Analysis_Summary/SampleMetricsReport.txt"
failureMarkerFile: "./failure.txt"
sampleSheet:
filePath: "SampleSheet.csv"
jointFiles:
snvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.sample.genome.vcf, Optional"
svFiles: "{sampleId.DNA}/{sampleId.DNA}_Amplifications.vcf, Optional"
sampleFiles:
tumorPairId:
alignmentFiles:
dnaBamFile: "{sampleId.DNA}/MergedBam/{sampleId.DNA}.bam, Optional"
dnaBaiFile: "{sampleId.DNA}/MergedBam/{sampleId.DNA}.bam.bai, Optional"
