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Results

Results

Results from the pipeline are organized in a structured directory format, making it easy to locate and analyze outputs.

Results Directory Structure

The results root is defined by ${OUTDIR}, which can be either the default location or a custom path specified when launching the workflow. The directory structure is as follows:

├── Actionable
├── annotation
├── log
├── Test
├── Test_N2D_E
├── Test_T1D_E
├── Test_T1R_T
├── qc
└── successful.txt

Description of Contents

1. Actionable/

  • *.unionSomaticVarsFull.txt – Union of somatic variants from multiple variant callers.
  • *.mutationalSignature.pdf – Mutational signature plots derived from COSMIC signatures.
  • *.actionable.fusion.txt – Actionable fusion calls from consensus fusion detection.
  • fusion.actionable.txt – Summary of actionable fusion results across samples.

2. annotation/

  • AnnotationInput – Base variant list before annotation.
  • AnnotationInput.anno – Primary annotation file with basic functional effects.
  • AnnotationInput.sift – SIFT scores predicting functional impact.
  • AnnotationInput.candl – CAN-DL annotation results.
  • AnnotationInput.civic – CIViC (Clinical Interpretation of Variants in Cancer) annotations.
  • AnnotationInput.clinvar – ClinVar clinical significance annotations.
  • AnnotationInput.docm – Database of Curated Mutations results.
  • AnnotationInput_final – Consolidated annotation file after merging data sources.
  • AnnotationInput.hgmd – Human Gene Mutation Database annotations.
  • AnnotationInput.match – Matched database entries.
  • AnnotationInput.mcg – MCG (Molecular Cancer Genetics) annotations.
  • AnnotationInput.tcc – TCC-specific annotations.
  • AnnotationInput.cadd – CADD (Combined Annotation Dependent Depletion) scores.
  • AnnotationInput.clinseq – ClinSeq annotations.
  • AnnotationInput.cosmic – COSMIC (Catalogue of Somatic Mutations in Cancer) annotations.
  • AnnotationInput.gene – Gene-level annotations.
  • AnnotationInput.pcg – PCG (Precision Cancer Genomics) annotations.
  • versions.yml – Software and database version information.
  • *.Annotations.coding.rare.txt – Coding variants that are rare in the population with MAF < 0.05.
  • *.Annotations.final.txt – Final comprehensive variant annotation file.

3. log/

  • trace.YYYY-MM-DD_HH-MM-SS.txt – Nextflow trace file showing per-process execution stats (CPU, memory, time, etc.).
  • report_YYYY-MM-DD_HH-MM-SS.html – Interactive Nextflow HTML report summarizing execution, resources, and task breakdowns.
  • timeline_YYYY-MM-DD_HH-MM-SS.html – Visual timeline showing when each process ran and for how long.
  • dag.YYYY-MM-DD_HH-MM-SS.png – Directed acyclic graph of the workflow steps and their dependencies.
  • bco_YYYY-MM-DD_HH-MM-SS.json – BioCompute Object (BCO) file capturing workflow provenance and metadata.
  • manifest_YYYY-MM-DD_HH-MM-SS.json – Manifest describing run inputs, parameters, and environment details.

4. Test_N2D_E/

  • calls/ – Variant call files generated for the matched normal sample.
  • HLA/ – HLA typing results.
  • Test_N2D_E.final.bam – Final aligned GATK BAM file for the matched normal sample.
  • Test_N2D_E.final.bam.bai – Index file for the final BAM.
  • Test_N2D_E.final.squeeze.bam – BAM for IGV.
  • Test_N2D_E.final.squeeze.bam.bai – Index file for the squeezed BAM.
  • qc/ – Quality control metrics and reports.
  • TCellExTRECT/ – T cell infiltration/extrect analysis results.
  • verifyBamID/ – Results from VerifyBamID for contamination/identity checks.

5. Test_T1D_E/

  • calls/ – Variant call files for the tumor DNA sample.
  • cnvkit/ – CNVkit copy-number analysis results.
  • HLA/ – HLA typing results.
  • Test_T1D_E.final.bam – Final aligned GATK BAM file for the tumor DNA sample.
  • Test_T1D_E.final.bam.bai – Index file for the final BAM.
  • Test_T1D_E.final.squeeze.bam – BAM for IGV viewing.
  • Test_T1D_E.final.squeeze.bam.bai – Index file for the squeezed BAM.
  • NeoAntigen/ – Predicted neoantigen results.
  • qc/ – Quality control metrics and reports.
  • sequenza/ – Sequenza purity/ploidy estimation results.
  • TCellExTRECT/ – T cell infiltration/extrect analysis results.
  • verifyBamID/ – VerifyBamID contamination/identity check results.

6. Test_T1R_T/

  • calls/ – Variant calls from RNA-seq data.
  • fusion/ – Fusion detection results.
  • HLA/ – HLA typing results from RNA data.
  • Test_T1R_T.final.bam / .bai – Final aligned RNA BAM + index.
  • Test_T1R_T.final.squeeze.bam / .bai – Squeezed BAM for IGV + index.
  • qc/ – QC metrics/reports for RNA-seq.
  • RSEM_ENS/ – RSEM expression quantification.

7. qc/

  • Test.transcriptCoverage.png – Transcript coverage plot for RNA-seq libraries.
  • Test.RnaSeqQC.txt – RNA-seq QC metrics table.
  • Test.circos.png – Circos plot summarizing structural variations and genome-wide metrics across libraries within the case.
  • Test.hotspot_coverage.png – Coverage at hotspot variant locations across libraries within the case.
  • Test.consolidated_QC.txt – Consolidated QC summary combining results from all libraries for the patient.
  • multiqc_report.html – Aggregated QC metrics from multiple tools in HTML format.
  • Test.config.*.txt – Tool versions used for each run.
  • genotyping.html – Genotyping QC results in HTML format to send out pipeline completion emails.
  • Test.genotyping.txt – Genotyping QC results in text format.

8. successful.txt