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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
msiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
snvFiles: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional
cnvFiles:
- Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional
- Logs_Intermediates/LrCalculator/{sampleId.DNA}/{sampleId.DNA}_DragenExonCNV.vcf, 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
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
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
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
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
msiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
snvFiles: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional
cnvFiles:
- Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional
- Logs_Intermediates/LrCalculator/{sampleId.DNA}/{sampleId.DNA}_DragenExonCNV.vcf, 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
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
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
snvFiles: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional
cnvFiles:
- Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional
- Logs_Intermediates/LrCalculator/{sampleId.DNA}/{sampleId.DNA}_DragenExonCNV.vcf, 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
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
Connected Insights directly supports the following pipelines:
Pipeline Name and YAML
Support (Local Storage / ICA)
Local Storage and ICA
Local Storage and ICA
Local Storage
Local Storage
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage
Local Storage
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
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
msiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
snvFiles: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional
cnvFiles:
- Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional
- Logs_Intermediates/LrCalculator/{sampleId.DNA}/{sampleId.DNA}_DragenExonCNV.vcf, 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
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
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
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
pipeline:
type: WGS
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.RNA}.time_metrics.csv, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.time_metrics.csv, Optional"
failureMarkerFile: "./failure.txt"
sampleSheet:
filePath: SampleSheet.csv
columnAliases:
sampleType: DnaOrRna
sampleId: Sample_ID
pairId: PairID
jointFiles:
snvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
cnvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
svFiles:
- "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
- "{sampleId.DNA}.sv.vcf.gz, Optional"
- "{prefix}/{prefix}.sv.vcf.gz, Optional"
- "{prefix}.sv.vcf.gz, Optional"
rnaFusionFiles:
- "{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
- "{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
- "{prefix}/{prefix}.fusion_candidates.vcf.gz, Optional"
- "{prefix}.fusion_candidates.vcf.gz, Optional"
rnaSpliceFiles:
- "{sampleId.RNA}/{sampleId.RNA}.splice_variants.vcf.gz, Optional"
- "{sampleId.RNA}.splice_variants.vcf.gz, Optional"
- "{prefix}/{prefix}.splice_variants.vcf.gz, Optional"
- "{prefix}.splice_variants.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.mapping_metrics.csv, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}.sv_metrics.csv, Optional"
- "{sampleId.RNA}.mapping_metrics.csv, Optional"
- "{sampleId.RNA}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.vc_metrics.csv, Optional"
- "{prefix}/{prefix}.cnv_metrics.csv, Optional"
- "{prefix}/{prefix}.sv_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}.vc_metrics.csv, Optional"
- "{prefix}.cnv_metrics.csv, Optional"
- "{prefix}.sv_metrics.csv, Optional"
sampleFiles:
tumorPairId:
alignmentFiles:
dnaBamFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
- "{sampleId.DNA}_tumor.bam, Optional"
- "{prefix}/{prefix}_tumor.bam, Optional"
- "{prefix}_tumor.bam, Optional"
dnaBaiFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
- "{sampleId.DNA}_tumor.bam.bai, Optional"
- "{prefix}/{prefix}_tumor.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"
rnaBamFile:
- "{sampleId.RNA}/{sampleId.RNA}_tumor.bam, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.bam, Optional"
- "{sampleId.RNA}_tumor.bam, Optional"
- "{sampleId.RNA}.bam, Optional"
- "{prefix}_tumor.bam, Optional"
- "{prefix}.bam, Optional"
rnaBaiFile:
- "{sampleId.RNA}/{sampleId.RNA}_tumor.bam.bai, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional"
- "{sampleId.RNA}_tumor.bam.bai, Optional"
- "{sampleId.RNA}.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"
- "{prefix}.bam.bai, Optional"
pipeline:
type: WGS
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.RNA}.time_metrics.csv, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.time_metrics.csv, Optional"
failureMarkerFile: "./failure.txt"
sampleSheet:
filePath: SampleSheet.csv
columnAliases:
sampleType: DnaOrRna
sampleId: Sample_ID
pairId: PairID
jointFiles:
snvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
cnvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
svFiles:
- "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
- "{sampleId.DNA}.sv.vcf.gz, Optional"
- "{prefix}/{prefix}.sv.vcf.gz, Optional"
- "{prefix}.sv.vcf.gz, Optional"
rnaFusionFiles:
- "{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
- "{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
- "{prefix}/{prefix}.fusion_candidates.vcf.gz, Optional"
- "{prefix}.fusion_candidates.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.mapping_metrics.csv, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}.sv_metrics.csv, Optional"
- "{sampleId.RNA}.mapping_metrics.csv, Optional"
- "{sampleId.RNA}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.vc_metrics.csv, Optional"
- "{prefix}/{prefix}.cnv_metrics.csv, Optional"
- "{prefix}/{prefix}.sv_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}.vc_metrics.csv, Optional"
- "{prefix}.cnv_metrics.csv, Optional"
- "{prefix}.sv_metrics.csv, Optional"
sampleFiles:
tumorPairId:
alignmentFiles:
dnaBamFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
- "{sampleId.DNA}_tumor.bam, Optional"
- "{prefix}/{prefix}_tumor.bam, Optional"
- "{prefix}_tumor.bam, Optional"
dnaBaiFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
- "{sampleId.DNA}_tumor.bam.bai, Optional"
- "{prefix}/{prefix}_tumor.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"
rnaBamFile:
- "{sampleId.RNA}/{sampleId.RNA}_tumor.bam, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.bam, Optional"
- "{sampleId.RNA}_tumor.bam, Optional"
- "{sampleId.RNA}.bam, Optional"
- "{prefix}_tumor.bam, Optional"
- "{prefix}.bam, Optional"
rnaBaiFile:
- "{sampleId.RNA}/{sampleId.RNA}_tumor.bam.bai, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional"
- "{sampleId.RNA}_tumor.bam.bai, Optional"
- "{sampleId.RNA}.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"
- "{prefix}.bam.bai, Optional"
pipeline:
type: WGS
sampleType: RNA
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.RNA}.time_metrics.csv, Optional"
failureMarkerFile: ./failure.txt
sampleSheet:
filePath: SampleSheet.csv
jointFiles:
snvFiles:
- "{sampleId.RNA}/{sampleId.RNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
- "{sampleId.RNA}.hard-filtered.vcf.gz, Optional"
rnaGeneExpressionFiles:
- "{sampleId.RNA}/{sampleId.RNA}.quant.genes.sf, Optional"
- "{prefix}/{prefix}.quant.genes.sf, Optional"
- "{sampleId.RNA}.quant.genes.sf, Optional"
- "{prefix}.quant.genes.sf, Optional"
rnaFusionFiles:
- "{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
- "{prefix}/{prefix}.fusion_candidates.vcf.gz, Optional"
- "{prefix}.fusion_candidates.vcf.gz, Optional"
- "{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.RNA}/{sampleId.RNA}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{sampleId.RNA}.mapping_metrics.csv, Optional"
sampleFiles:
tumorPairId:
alignmentFiles:
rnaBamFile:
- "{sampleId.RNA}/{sampleId.RNA}.bam, Optional"
- "{prefix}/{prefix}.bam, Optional"
- "{prefix}.bam, Optional"
- "{sampleId.RNA}.bam, Optional"
rnaBaiFile:
- "{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional"
- "{prefix}/{prefix}.bam.bai, Optional"
- "{prefix}.bam.bai, Optional"
- "{sampleId.RNA}.bam.bai, Optional"
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
pipeline:
type: WGS
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.RNA}.time_metrics.csv, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.time_metrics.csv, Optional"
failureMarkerFile: "./failure.txt"
sampleSheet:
filePath: SampleSheet.csv
columnAliases:
sampleType: DnaOrRna
sampleId: Sample_ID
pairId: PairID
jointFiles:
snvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
cnvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
svFiles:
- "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
- "{sampleId.DNA}.sv.vcf.gz, Optional"
- "{prefix}/{prefix}.sv.vcf.gz, Optional"
- "{prefix}.sv.vcf.gz, Optional"
rnaFusionFiles:
- "{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
- "{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
- "{prefix}/{prefix}.fusion_candidates.vcf.gz, Optional"
- "{prefix}.fusion_candidates.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.mapping_metrics.csv, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}.sv_metrics.csv, Optional"
- "{sampleId.RNA}.mapping_metrics.csv, Optional"
- "{sampleId.RNA}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.vc_metrics.csv, Optional"
- "{prefix}/{prefix}.cnv_metrics.csv, Optional"
- "{prefix}/{prefix}.sv_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}.vc_metrics.csv, Optional"
- "{prefix}.cnv_metrics.csv, Optional"
- "{prefix}.sv_metrics.csv, Optional"
sampleFiles:
tumorPairId:
alignmentFiles:
dnaBamFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
- "{sampleId.DNA}_tumor.bam, Optional"
- "{prefix}/{prefix}_tumor.bam, Optional"
- "{prefix}_tumor.bam, Optional"
dnaBaiFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
- "{sampleId.DNA}_tumor.bam.bai, Optional"
- "{prefix}/{prefix}_tumor.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"
rnaBamFile:
- "{sampleId.RNA}/{sampleId.RNA}_tumor.bam, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.bam, Optional"
- "{sampleId.RNA}_tumor.bam, Optional"
- "{sampleId.RNA}.bam, Optional"
- "{prefix}_tumor.bam, Optional"
- "{prefix}.bam, Optional"
rnaBaiFile:
- "{sampleId.RNA}/{sampleId.RNA}_tumor.bam.bai, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional"
- "{sampleId.RNA}_tumor.bam.bai, Optional"
- "{sampleId.RNA}.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"
- "{prefix}.bam.bai, Optional"
pipeline:
type: WGS
sampleType: RNA
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.RNA}.time_metrics.csv, Optional"
failureMarkerFile: ./failure.txt
sampleSheet:
filePath: SampleSheet.csv
jointFiles:
snvFiles:
- "{sampleId.RNA}/{sampleId.RNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
- "{sampleId.RNA}.hard-filtered.vcf.gz, Optional"
rnaGeneExpressionFiles:
- "{sampleId.RNA}/{sampleId.RNA}.quant.genes.sf, Optional"
- "{prefix}/{prefix}.quant.genes.sf, Optional"
- "{sampleId.RNA}.quant.genes.sf, Optional"
- "{prefix}.quant.genes.sf, Optional"
rnaFusionFiles:
- "{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
- "{prefix}/{prefix}.fusion_candidates.vcf.gz, Optional"
- "{prefix}.fusion_candidates.vcf.gz, Optional"
- "{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.RNA}/{sampleId.RNA}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{sampleId.RNA}.mapping_metrics.csv, Optional"
sampleFiles:
tumorPairId:
alignmentFiles:
rnaBamFile:
- "{sampleId.RNA}/{sampleId.RNA}.bam, Optional"
- "{prefix}/{prefix}.bam, Optional"
- "{prefix}.bam, Optional"
- "{sampleId.RNA}.bam, Optional"
rnaBaiFile:
- "{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional"
- "{prefix}/{prefix}.bam.bai, Optional"
- "{prefix}.bam.bai, Optional"
- "{sampleId.RNA}.bam.bai, Optional"
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
pipeline:
type: WGS
sampleType: DNA
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"
failureMarkerFile: "./failure.txt"
jointFiles:
purityPloidyFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
gisFile:
- "{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional"
- "{prefix}/{prefix}.gis.json, Optional"
- "{prefix}.gis.json, Optional"
- "{sampleId.DNA}.gis.json, Optional"
msiFile:
- "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
- "{prefix}/{prefix}.microsat_output.json, Optional"
- "{prefix}.microsat_output.json, Optional"
- "{sampleId.DNA}.microsat_output.json, Optional"
tmbFile:
- "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
- "{prefix}/{prefix}.tmb.metrics.csv, Optional"
- "{prefix}.tmb.metrics.csv, Optional"
- "{sampleId.DNA}.tmb.metrics.csv, Optional"
snvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
- "{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
cnvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
svFiles:
- "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
- "{prefix}/{prefix}.sv.vcf.gz, Optional"
- "{prefix}.sv.vcf.gz, Optional"
- "{sampleId.DNA}.sv.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.vc_metrics.csv, Optional"
- "{prefix}/{prefix}.cnv_metrics.csv, Optional"
- "{prefix}/{prefix}.sv_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}.vc_metrics.csv, Optional"
- "{prefix}.cnv_metrics.csv, Optional"
- "{prefix}.sv_metrics.csv, Optional"
- "{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}.sv_metrics.csv, Optional"
sampleFiles:
tumorPairId:
visualizationFiles:
coverageFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}/{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
ballelesFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}/{prefix}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}.tumor.baf.bedgraph.gz, Optional"
alignmentFiles:
dnaBamFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
- "{sampleId.DNA}_tumor.bam, Optional"
- "{prefix}/{prefix}_tumor.bam, Optional"
- "{prefix}_tumor.bam, Optional"
dnaBaiFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
- "{sampleId.DNA}_tumor.bam.bai, Optional"
- "{prefix}/{prefix}_tumor.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"
pipeline:
type: WGS
sampleType: RNA
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{sampleId.RNA}/{sampleId.RNA}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.RNA}.time_metrics.csv, Optional"
failureMarkerFile: ./failure.txt
sampleSheet:
filePath: SampleSheet.csv
jointFiles:
snvFiles:
- "{sampleId.RNA}/{sampleId.RNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
- "{sampleId.RNA}.hard-filtered.vcf.gz, Optional"
rnaGeneExpressionFiles:
- "{sampleId.RNA}/{sampleId.RNA}.quant.genes.sf, Optional"
- "{prefix}/{prefix}.quant.genes.sf, Optional"
- "{sampleId.RNA}.quant.genes.sf, Optional"
- "{prefix}.quant.genes.sf, Optional"
rnaFusionFiles:
- "{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
- "{prefix}/{prefix}.fusion_candidates.vcf.gz, Optional"
- "{prefix}.fusion_candidates.vcf.gz, Optional"
- "{sampleId.RNA}.fusion_candidates.vcf.gz, Optional"
rnaSpliceFiles:
- "{sampleId.RNA}/{sampleId.RNA}.splice_variants.vcf.gz, Optional"
- "{sampleId.RNA}.splice_variants.vcf.gz, Optional"
- "{prefix}/{prefix}.splice_variants.vcf.gz, Optional"
- "{prefix}.splice_variants.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.RNA}/{sampleId.RNA}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{sampleId.RNA}.mapping_metrics.csv, Optional"
sampleFiles:
tumorPairId:
alignmentFiles:
rnaBamFile:
- "{sampleId.RNA}/{sampleId.RNA}.bam, Optional"
- "{prefix}/{prefix}.bam, Optional"
- "{prefix}.bam, Optional"
- "{sampleId.RNA}.bam, Optional"
rnaBaiFile:
- "{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional"
- "{prefix}/{prefix}.bam.bai, Optional"
- "{prefix}.bam.bai, Optional"
- "{sampleId.RNA}.bam.bai, Optional"
pipeline:
type: WGS
sampleType: DNA
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"
failureMarkerFile: "./failure.txt"
jointFiles:
purityPloidyFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
gisFile:
- "{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional"
- "{prefix}/{prefix}.gis.json, Optional"
- "{prefix}.gis.json, Optional"
- "{sampleId.DNA}.gis.json, Optional"
msiFile:
- "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
- "{prefix}/{prefix}.microsat_output.json, Optional"
- "{prefix}.microsat_output.json, Optional"
- "{sampleId.DNA}.microsat_output.json, Optional"
tmbFile:
- "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
- "{prefix}/{prefix}.tmb.metrics.csv, Optional"
- "{prefix}.tmb.metrics.csv, Optional"
- "{sampleId.DNA}.tmb.metrics.csv, Optional"
snvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
- "{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
cnvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
svFiles:
- "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
- "{prefix}/{prefix}.sv.vcf.gz, Optional"
- "{prefix}.sv.vcf.gz, Optional"
- "{sampleId.DNA}.sv.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.vc_metrics.csv, Optional"
- "{prefix}/{prefix}.cnv_metrics.csv, Optional"
- "{prefix}/{prefix}.sv_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}.vc_metrics.csv, Optional"
- "{prefix}.cnv_metrics.csv, Optional"
- "{prefix}.sv_metrics.csv, Optional"
- "{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}.sv_metrics.csv, Optional"
sampleFiles:
tumorPairId:
visualizationFiles:
coverageFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}/{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
ballelesFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}/{prefix}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}.tumor.baf.bedgraph.gz, Optional"
alignmentFiles:
dnaBamFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
- "{sampleId.DNA}_tumor.bam, Optional"
- "{prefix}/{prefix}_tumor.bam, Optional"
- "{prefix}_tumor.bam, Optional"
dnaBaiFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
- "{sampleId.DNA}_tumor.bam.bai, Optional"
- "{prefix}/{prefix}_tumor.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"
pipeline:
type: WGS
sampleType: DNA
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"
failureMarkerFile: "./failure.txt"
jointFiles:
purityPloidyFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
gisFile:
- "{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional"
- "{prefix}/{prefix}.gis.json, Optional"
- "{prefix}.gis.json, Optional"
- "{sampleId.DNA}.gis.json, Optional"
msiFile:
- "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
- "{prefix}/{prefix}.microsat_output.json, Optional"
- "{prefix}.microsat_output.json, Optional"
- "{sampleId.DNA}.microsat_output.json, Optional"
tmbFile:
- "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
- "{prefix}/{prefix}.tmb.metrics.csv, Optional"
- "{prefix}.tmb.metrics.csv, Optional"
- "{sampleId.DNA}.tmb.metrics.csv, Optional"
snvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
- "{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
cnvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
svFiles:
- "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
- "{prefix}/{prefix}.sv.vcf.gz, Optional"
- "{prefix}.sv.vcf.gz, Optional"
- "{sampleId.DNA}.sv.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.vc_metrics.csv, Optional"
- "{prefix}/{prefix}.cnv_metrics.csv, Optional"
- "{prefix}/{prefix}.sv_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}.vc_metrics.csv, Optional"
- "{prefix}.cnv_metrics.csv, Optional"
- "{prefix}.sv_metrics.csv, Optional"
- "{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}.sv_metrics.csv, Optional"
sampleFiles:
tumorPairId:
visualizationFiles:
coverageFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}/{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
ballelesFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}/{prefix}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}.tumor.baf.bedgraph.gz, Optional"
alignmentFiles:
dnaBamFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
- "{sampleId.DNA}_tumor.bam, Optional"
- "{prefix}/{prefix}_tumor.bam, Optional"
- "{prefix}_tumor.bam, Optional"
dnaBaiFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
- "{sampleId.DNA}_tumor.bam.bai, Optional"
- "{prefix}/{prefix}_tumor.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"
pipeline:
type: WGS
sampleType: DNA
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"
failureMarkerFile: "./failure.txt"
jointFiles:
purityPloidyFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
gisFile:
- "{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional"
- "{prefix}/{prefix}.gis.json, Optional"
- "{prefix}.gis.json, Optional"
- "{sampleId.DNA}.gis.json, Optional"
msiFile:
- "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
- "{prefix}/{prefix}.microsat_output.json, Optional"
- "{prefix}.microsat_output.json, Optional"
- "{sampleId.DNA}.microsat_output.json, Optional"
tmbFile:
- "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
- "{prefix}/{prefix}.tmb.metrics.csv, Optional"
- "{prefix}.tmb.metrics.csv, Optional"
- "{sampleId.DNA}.tmb.metrics.csv, Optional"
snvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
- "{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
cnvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
svFiles:
- "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
- "{prefix}/{prefix}.sv.vcf.gz, Optional"
- "{prefix}.sv.vcf.gz, Optional"
- "{sampleId.DNA}.sv.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.vc_metrics.csv, Optional"
- "{prefix}/{prefix}.cnv_metrics.csv, Optional"
- "{prefix}/{prefix}.sv_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}.vc_metrics.csv, Optional"
- "{prefix}.cnv_metrics.csv, Optional"
- "{prefix}.sv_metrics.csv, Optional"
- "{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}.sv_metrics.csv, Optional"
sampleFiles:
tumorPairId:
visualizationFiles:
coverageFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}/{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
ballelesFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}/{prefix}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}.tumor.baf.bedgraph.gz, Optional"
alignmentFiles:
dnaBamFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
- "{sampleId.DNA}_tumor.bam, Optional"
- "{prefix}/{prefix}_tumor.bam, Optional"
- "{prefix}_tumor.bam, Optional"
dnaBaiFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
- "{sampleId.DNA}_tumor.bam.bai, Optional"
- "{prefix}/{prefix}_tumor.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"
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"
pipeline:
type: WGS
sampleType: DNA
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"
failureMarkerFile: "./failure.txt"
jointFiles:
purityPloidyFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
gisFile:
- "{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional"
- "{prefix}/{prefix}.gis.json, Optional"
- "{prefix}.gis.json, Optional"
- "{sampleId.DNA}.gis.json, Optional"
msiFile:
- "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
- "{prefix}/{prefix}.microsat_output.json, Optional"
- "{prefix}.microsat_output.json, Optional"
- "{sampleId.DNA}.microsat_output.json, Optional"
tmbFile:
- "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
- "{prefix}/{prefix}.tmb.metrics.csv, Optional"
- "{prefix}.tmb.metrics.csv, Optional"
- "{sampleId.DNA}.tmb.metrics.csv, Optional"
snvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
- "{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
cnvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
svFiles:
- "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
- "{prefix}/{prefix}.sv.vcf.gz, Optional"
- "{prefix}.sv.vcf.gz, Optional"
- "{sampleId.DNA}.sv.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.vc_metrics.csv, Optional"
- "{prefix}/{prefix}.cnv_metrics.csv, Optional"
- "{prefix}/{prefix}.sv_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}.vc_metrics.csv, Optional"
- "{prefix}.cnv_metrics.csv, Optional"
- "{prefix}.sv_metrics.csv, Optional"
- "{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}.sv_metrics.csv, Optional"
sampleFiles:
tumorPairId:
visualizationFiles:
coverageFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}/{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
ballelesFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}/{prefix}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}.tumor.baf.bedgraph.gz, Optional"
alignmentFiles:
dnaBamFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
- "{sampleId.DNA}_tumor.bam, Optional"
- "{prefix}/{prefix}_tumor.bam, Optional"
- "{prefix}_tumor.bam, Optional"
dnaBaiFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
- "{sampleId.DNA}_tumor.bam.bai, Optional"
- "{prefix}/{prefix}_tumor.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"
pipeline:
type: WGS
sampleType: DNA
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"
failureMarkerFile: "./failure.txt"
jointFiles:
purityPloidyFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
gisFile:
- "{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional"
- "{prefix}/{prefix}.gis.json, Optional"
- "{prefix}.gis.json, Optional"
- "{sampleId.DNA}.gis.json, Optional"
msiFile:
- "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
- "{prefix}/{prefix}.microsat_output.json, Optional"
- "{prefix}.microsat_output.json, Optional"
- "{sampleId.DNA}.microsat_output.json, Optional"
tmbFile:
- "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
- "{prefix}/{prefix}.tmb.metrics.csv, Optional"
- "{prefix}.tmb.metrics.csv, Optional"
- "{sampleId.DNA}.tmb.metrics.csv, Optional"
snvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
- "{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
cnvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
svFiles:
- "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
- "{prefix}/{prefix}.sv.vcf.gz, Optional"
- "{prefix}.sv.vcf.gz, Optional"
- "{sampleId.DNA}.sv.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.vc_metrics.csv, Optional"
- "{prefix}/{prefix}.cnv_metrics.csv, Optional"
- "{prefix}/{prefix}.sv_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}.vc_metrics.csv, Optional"
- "{prefix}.cnv_metrics.csv, Optional"
- "{prefix}.sv_metrics.csv, Optional"
- "{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}.sv_metrics.csv, Optional"
sampleFiles:
tumorPairId:
visualizationFiles:
coverageFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}/{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
ballelesFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}/{prefix}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}.tumor.baf.bedgraph.gz, Optional"
alignmentFiles:
dnaBamFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
- "{sampleId.DNA}_tumor.bam, Optional"
- "{prefix}/{prefix}_tumor.bam, Optional"
- "{prefix}_tumor.bam, Optional"
dnaBaiFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
- "{sampleId.DNA}_tumor.bam.bai, Optional"
- "{prefix}/{prefix}_tumor.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"
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"
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
snvFiles: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional
cnvFiles:
- Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional
- Logs_Intermediates/LrCalculator/{sampleId.DNA}/{sampleId.DNA}_DragenExonCNV.vcf, 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
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
pipeline:
type: WGS
sampleType: DNA
successMarkerFile:
- "{prefix}/{prefix}.time_metrics.csv, Optional"
- "{prefix}.time_metrics.csv, Optional"
- "{sampleId.DNA}.time_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.time_metrics.csv, Optional"
failureMarkerFile: "./failure.txt"
jointFiles:
purityPloidyFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
gisFile:
- "{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional"
- "{sampleId.DNA}.gis.json, Optional"
- "{prefix}/{prefix}.gis.json, Optional"
- "{prefix}.gis.json, Optional"
msiFile:
- "{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional"
- "{sampleId.DNA}.microsat_output.json, Optional"
- "{prefix}/{prefix}.microsat_output.json, Optional"
- "{prefix}.microsat_output.json, Optional"
tmbFile:
- "{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional"
- "{sampleId.DNA}.tmb.metrics.csv, Optional"
- "{prefix}/{prefix}.tmb.metrics.csv, Optional"
- "{prefix}.tmb.metrics.csv, Optional"
snvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{sampleId.DNA}.hard-filtered.vcf.gz, Optional"
- "{prefix}/{prefix}.hard-filtered.vcf.gz, Optional"
- "{prefix}.hard-filtered.vcf.gz, Optional"
cnvFiles:
- "{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{sampleId.DNA}.cnv.vcf.gz, Optional"
- "{prefix}/{prefix}.cnv.vcf.gz, Optional"
- "{prefix}.cnv.vcf.gz, Optional"
svFiles:
- "{sampleId.DNA}/{sampleId.DNA}.sv.vcf.gz, Optional"
- "{sampleId.DNA}.sv.vcf.gz, Optional"
- "{prefix}/{prefix}.sv.vcf.gz, Optional"
- "{prefix}.sv.vcf.gz, Optional"
metricsQCFile:
- "{sampleId.DNA}/{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.sv_metrics.csv, Optional"
- "{sampleId.DNA}.mapping_metrics.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_tumor.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics_normal.csv, Optional"
- "{sampleId.DNA}.wgs_coverage_metrics.csv, Optional"
- "{sampleId.DNA}.vc_metrics.csv, Optional"
- "{sampleId.DNA}.cnv_metrics.csv, Optional"
- "{sampleId.DNA}.sv_metrics.csv, Optional"
- "{prefix}/{prefix}.mapping_metrics.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}/{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}/{prefix}.vc_metrics.csv, Optional"
- "{prefix}/{prefix}.cnv_metrics.csv, Optional"
- "{prefix}/{prefix}.sv_metrics.csv, Optional"
- "{prefix}.mapping_metrics.csv, Optional"
- "{prefix}.wgs_coverage_metrics_tumor.csv, Optional"
- "{prefix}.wgs_coverage_metrics_normal.csv, Optional"
- "{prefix}.wgs_coverage_metrics.csv, Optional"
- "{prefix}.vc_metrics.csv, Optional"
- "{prefix}.cnv_metrics.csv, Optional"
- "{prefix}.sv_metrics.csv, Optional"
sampleFiles:
tumorPairId:
visualizationFiles:
coverageFiles:
- "{sampleId.DNA}/{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{sampleId.DNA}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}/{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
- "{prefix}.tumor.target.counts.gc-corrected.gz, Optional"
ballelesFiles:
- "{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}.tumor.baf.bedgraph.gz, Optional"
- "{prefix}/{prefix}.tumor.baf.bedgraph.gz, Optional"
- "{sampleId.DNA}/{sampleId.DNA}.tumor.baf.bedgraph.gz, Optional"
alignmentFiles:
dnaBamFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam, Optional"
- "{sampleId.DNA}_tumor.bam, Optional"
- "{prefix}/{prefix}_tumor.bam, Optional"
- "{prefix}_tumor.bam, Optional"
dnaBaiFile:
- "{sampleId.DNA}/{sampleId.DNA}_tumor.bam.bai, Optional"
- "{sampleId.DNA}_tumor.bam.bai, Optional"
- "{prefix}/{prefix}_tumor.bam.bai, Optional"
- "{prefix}_tumor.bam.bai, Optional"