Single Node Analysis Output Folder Structure

This section describes the content of output folders generated from analysis run on a single node.

Single output folder structure is as follows.:

Logs_Intermediates

AdditionalSarjMetrics— Contains per pair ID calculations to support the PCT_TARGET_250X metric.

Annotation—Contains outputs for small variant annotation.

Subfolders per sample ID—Contains the aligned small variants JSON.

CombinedVariantOutput

Subfolders per pair ID—Contains the combined variant output TSV files.

A combined output log file.

Contamination

Subfolders per DNA sample ID—Contains the contamination metrics JSON file and output logs.

DnaDragenCaller

Subfolders per sample ID—Contains the aligned BAM and index files, small variant VCF and gVCF, copy number variant VCF, MSI JSON, and QC outputs in CSV format.

DnaDragenExonCNVCaller

Subfolders per DNA sample ID—Contains the exon-level CNV JSON, along withthe supporting calculation, and the QC files.

DnaFastqValidation—Contains the FASTQ validation output log for DNA samples.

FastqDownsample

Subfolders per RNA sample ID—Contains FASTQ files and output logs.

FastqDownsample output

Gis—Contains GIS-related files for HRD samples.

Subfolders per HRD sample ID—Contains the GIS JSON, the along with supporting calculation, and the QC files.

LrAnnotation

Subfolders per DNA sample ID—Contains the annotated exon-level CNV JSON.

LrCalculator

Subfolders per DNA sample ID—Contains the exon-level CNV VCF.

MetricsOutput

Subfolders per pair ID—Contains the metrics output TSV files.

A combined output log file.

ResourceVerification—Contains the resource file checksum verification logs.

RnaAnnotation

Subfolders per RNA sample ID—Contains the annotated splice variant JSON.

RnaDragenCaller

Subfolders per sample ID—Contains the aligned BAM, fusion candidates CSV, and QC outputs in CSV format.

RnaFastqValidation—Contains the FASTQ validation output log for RNA samples.

RnaFusion

Subfolders per RNA sample ID—Contains the All Fusions CSV and Fusion Processor logs.

RnaQcMetrics

Subfolders per RNA sample ID—Contains the RNA QC metrics JSON.

RnaSpliceVariantCalling

Subfolders per RNA sample ID—Contains the splice variants VCF.

Run QC—Contains the Run QC metrics JSON, Intermediate Run QC metrics JSON, and log file.

SampleAnalysisResults

Subfolders per pair ID—Contains the Sample Analysis Results JSON and detailed log file.

SampleSheetValidation—Contains the Intermediate sample sheet and validation log.

Tmb

Subfolders per DNA sample ID—Contains the TMB metrics CSV, TMB trace TSV, and related files and logs.

passing_sample_steps.json—Contains the steps passed for each sample ID.

pipeline_trace.txt—Contains a summary and troubleshooting file that lists each Nextflow task executed and the statusstatus (for example, COMPLETED or FAILED).

run.log—Contains a complete trace-level log file describing the Nextflow pipeline execution.

run_report.html—Contains high-level run statistics (performance, usage, etc.)

run_timeline.html—Contains timeline-related information about the analysis run.

Results

Metrics Output TSV (all pair IDs)

Pair ID—The following outputs are produced for each sample:

Combined Variant Output TSV

Metrics Output TSV

TMB Trace TSV

Small Variant Genome VCF

Small Variant Genome Annotated JSON

Copy Number Variant VCF

GIS JSON

Exon-level CNV VCF

Exon-level CNV Annotated JSON

All Fusion CSV

Splice Variant VCF

Splice Variant Annotated JSON