pipeline:
successMarkerFile: "Reports/MetricsOutput.tsv"
failureMarkerFile: "./failure.txt"
sampleSheet:
filePath: "SampleSheet.csv"
columnAliases:
sampleId: Sample_ID
sampleType: Manifest
caseId: Pair_ID
disease:
id: Tumor_Type
name: Sample_Description
jointFiles:
msiFile: "Logs_Intermediates/DNA_IntermediateFiles/MSI/{sampleId.DNA}_MSI.json, Optional"
snvFiles: "{sampleId.DNA}/{sampleId.DNA}_SmallVariants.genome.vcf, Optional"
cnvFiles: "{sampleId.DNA}/{sampleId.DNA}_CopyNumberVariants.vcf, Optional"
rnaSpliceFiles: "Logs_Intermediates/RNA_IntermediateFiles/SpliceVariantCalling/{sampleId.RNA}_SpliceVariants.vcf, Optional"
rnaFusionFiles: "Logs_Intermediates/RNA_IntermediateFiles/FusionCalling/{sampleId.RNA}_Fusions.csv, Optional"
metricsQCFile: "Reports/MetricsOutput.tsv"
sampleFiles:
tumorPairId:
alignmentFiles:
dnaBamFile: "Logs_Intermediates/DNA_IntermediateFiles/Alignment/{sampleId.DNA}.bam, Optional"
dnaBaiFile: "Logs_Intermediates/DNA_IntermediateFiles/Alignment/{sampleId.DNA}.bam.bai, Optional"
rnaBamFile: "Logs_Intermediates/RNA_IntermediateFiles/Alignment/{sampleId.RNA}.bam, Optional"
rnaBaiFile: "Logs_Intermediates/RNA_IntermediateFiles/Alignment/{sampleId.RNA}.bam.bai, Optional"