pipeline:
type: TSO500
successMarkerFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
failureMarkerFile: ./failure.txt
sampleSheet:
filePath: SampleSheet.csv
jointFiles:
purityPloidyFiles: Logs_Intermediates/CombinedVariantOutput/{pairId}/{pairId}_CombinedVariantOutput.tsv, Optional
gisFile: Logs_Intermediates/Gis/{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional
msiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
lohFiles:
- Logs_Intermediates/Gis/{sampleId.DNA}/{sampleId.DNA}.abcn_genes.tsv, Optional
snvFiles: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional
cnvFiles:
- Logs_Intermediates/Gis/{sampleId.DNA}/{sampleId.DNA}.abcn_annotated.vcf, Optional
- Logs_Intermediates/LrCalculator/{sampleId.DNA}/{sampleId.DNA}_DragenExonCNV.vcf, Optional
- Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional
rnaSpliceFiles: Logs_Intermediates/RnaSpliceVariantCalling/{sampleId.RNA}/{sampleId.RNA}_SpliceVariants.vcf, Optional
rnaFusionFiles:
- Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional
- Logs_Intermediates/RnaFusion/{sampleId.RNA}/{sampleId.RNA}_AllFusions.csv, Optional
metricsQCFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
sampleFiles:
tumorPairId:
visualizationFiles:
coverageFiles: Logs_Intermediates/DnaDragenExonCnvCaller/{sampleId.DNA}/{sampleId.DNA}.target.counts.gc-corrected.gz, Optional
ballelesFiles: Logs_Intermediates/Gis/{sampleId.DNA}/{sampleId.DNA}.baf.bedgraph.gz, Optional
alignmentFiles:
dnaBamFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.bam, Optional
dnaBaiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.bam.bai, Optional
rnaBamFile: Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.bam, Optional
rnaBaiFile: Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional