phac-nml/typingQC: Output

Introduction

This document describes the outputs produced by the typingQC pipeline.

All paths are relative to the top-level results directory created by the pipeline. The pipeline generates per-sample reports, module-specific outputs, summary files, and a final IRIDA Next-compliant JSON output.

The IRIDA Next-compliant JSON output file will be named iridanext.output.json.gz and will be written to the top-level of the results directory. This file is compressed using GZIP and conforms to the IRIDA Next JSON output specifications.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

• SEQUENCEQC – Evaluates sequencing and assembly quality metrics.
• SISTRQC – Validates Salmonella serotype predictions.
• ECTYPERQC – Validates Escherichia serotype, toxin genes, and STX subtypes.
• EXCLUSIONS – Identifies why samples could not be typed.
• SEROTYPE – Generates final validated serotype assignments.
• Pipeline Information – Records pipeline execution metrics, versions, and reports.

SEQUENCEQC

Output files

• sequenceqc/
  • Per-sample CSV: ID_sequenceQC.csv
    • Contains sequencing QC metrics, PASS/WARNING/FAIL status, and detailed QC messages.

SISTRQC

Output files

• sistrqc/
  • Per-sample CSV: ID_sistrQC.csv
    • Contains Salmonella serovar predictions, QC status, and relevant warnings/errors.

ECTYPERQC

Output files

• ectyperqc/
  • Per-sample CSV: ID_ectyperQC.csv
    • Contains validated O/H serotypes, toxin genes, STX subtypes, and typingQC messages.

EXCLUSIONS

Output files

• exclusions/
  • Per-sample CSV: ID_exclusions.csv
    • Lists samples that could not be typed, along with the reason (e.g., unsupported species, missing mikrokondo file).

SEROTYPE

Output files

• serotype/
  • TypingQC_report.csv
    • Consolidates per-sample TypingQC results from all modules.
    • Contains final validated serotype, overall typingQC_message, and any manual verification approvals.

IRIDA Next Output

Output files

• /
  • IRIDA Next-compliant JSON output: iridanext.output.json.gz

Pipeline information

Output files

• pipeline_info/
  • Reports generated by Nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and pipeline_dag.dot/pipeline_dag.svg.
  • Reports generated by the pipeline: pipeline_report.html, pipeline_report.txt and software_versions.yml. The pipeline_report* files will only be present if the --email / --email_on_fail parameter's are used when running the pipeline.
  • Reformatted samplesheet files used as input to the pipeline: samplesheet.valid.csv.
  • Parameters used by the pipeline run: params.json.

Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.