Output folders

This section describes each output folder generated during analysis and where to find metric and analytic files when the pipeline is executed. The same output folder structure and content exist in ICA and BaseSpace Sequence Hub.

High-Level Folder Structure

• Run ID

  • TSO500_Nextflow_logs

    • _manifest.json

  • Results

    • _tags.json

  • Logs_intermediates

  • Errors—This folder is only present when analysis fails

TSO500_Nextflow_logs Folder Structure

The TSO_500_Nextflow_Logs provides information related to the execution of the pipeline on ICA as a whole and for specific nodes (when an analysis is split across multiple nodes). It contains files used to execute parts of the workflow on different nodes as well as records of the nextflow execution on those nodes.

• TSO_500_Nextflow_Logs

  • _manifest.json

Results Folder Structure

Contains the aggregated MetricsOutput.tsv file at the root level. Additionally, the Results folder contains a subfolder for each pair ID.

• Results

  • MetricsOutput.tsv

  • Sample_1

  • Sample_2

  • Sample_<#>

  • _tags.json

The Results subfolder contains the following files:

• Results

  • MetricsOutput.tsv

  • <Pair_id>

    • CombinedVariantOutput.tsv

    • <SampleName>_MetricsOutput.tsv

  • <DNA_Sample_id>

    • CopyNumberVariants.vcf

    • DNAMergedSmallVariants_Annotated.json.gz

    • MergedSmallVariants.genome.vcf

    • MergedSmallVariants.vcf

    • microstat_output.json

    • TMB_Trace.tsv

  • <RNA_Sample_id>

    • AllFusions.csv

    • RNA_Annotated.json.gz

    • SpliceVariants.vcf

Logs_intermediates Folder Structure

Contains folders for each submodule in the DRAGEN TSO 500 on ICA pipeline. The folders contain a copy of all the relevant files required to create the metric output files and report files, as well as the combined log files at the root level and subfolders for each sample.

• Logs_intermediates

  • DnaDragenCaller

  • AdditionalSarjMetrics

  • CombinedVariantOutput

  • FastqGeneration

  • MetricsOutput

  • DnaDragenExonCnvCaller

  • DnaFastqValidation

  • Gis

  • Tmb

  • SampleAnalysisResults

  • SampleSheetValidation

  • passing_sample_steps.json

  • RnaFusion

  • Contamination

  • Annotation

  • RnaAnnotation

  • RnaDragenCaller

  • RnaSpliceVariantCalling

  • RunQc

  • FastqDownsample

  • PassingSampleSteps

  • ResourceVerification

  • LrCalculator

  • LrAnnotation

  • RnaQcMetrics

  • RnaFastqValidation

Errors Folder Structure

Contains Errors.tsv. This file contains the summary of all the errors encountered during pipeline execution.

• Errors

  • Errors.tsv