Introduction Usage Output Results

Introduction

This document describes the output produced by the pipeline. After execution, the following directories will be created under the top-level results/ directory, each containing key output files necessary for downstream QC and reporting.

Pipeline overview

The pipeline is implemented with Nextflow and executes the following major steps:

  1. ThermoRawFileParser – Conversion of raw instrument files
  2. MSNBASEXIC – Extract chromatographic peaks and calculate per-analyte QC metrics
  3. Merge JSONs – Consolidation of individual QC metric JSONs into merged summaries
  4. MultiQC – Aggregation and visualization of QC metrics
  5. Pipeline information – Generation of execution reports and parameter logs

ThermoRawFileParser

Output files

  • thermorawfileparser/

    • *.mzML: .raw file convert to format suitable for downstream processing.

XIC results

Output files
  • msnbasexic/
    • Contains one .json file per sample and per analyte, named according to the QC metrics and sample ID (e.g. dmz_ppm_Day_5_mqc.json).
    • Format: structured JSON capturing extracted chromatographic metrics for each analyte, such as retention time, peak area, mass accuracy and FWHM.
    • These files represent the core QC outputs generated from XIC extraction and can be used for both individual review and longitudinal performance assessment.

Merge JSONs

Output files
  • mergejsons/
    • This folder contains JSON files summarizing QC metrics across all samples for each parameter. These are used by MultiQC for report generation.
    • Files include:
      • dmz_ppm_merged_mqc.json: Summary of mass accuracy deviations (Δm/z in ppm) for each analyte across samples.
      • FWHM_merged_mqc.json: Full Width at Half Maximum values for chromatographic peaks, used to assess peak sharpness and consistency.
      • Log2_Total_Area_merged_mqc.json: Log2-transformed total peak areas, serving as a proxy for relative analyte abundance and signal stability.
      • Observed_RT_sec_merged_mqc.json: Observed retention times (in seconds) across samples, useful for detecting RT drift over time.

Each of these merged JSON files consolidates multiple per-sample (or per-file) JSON outputs for the same QC metric into a single array. For example, all individual dmz_ppm.json fragments from different samples are combined into dmz_ppm_merged_mqc.json. This ensures that each parameter’s values across all samples are gathered in one file, formatted for seamless ingestion by MultiQC and unified visualization of QC trends.

MultiQC report

Output files

  • multiqc/

    • multiqc_report.html: Interactive HTML report aggregating XIC-derived tables and merged JSON metrics.
    • multiqc_data/: Directory containing raw data inputs for MultiQC, including the merged QC JSON files.

Pipeline information

Output files

  • pipeline_info/

    • Nextflow execution artifacts: execution_report.html, execution_timeline.html, execution_trace.txt, pipeline_dag.dot/pipeline_dag.svg
    • Pipeline software versions: nf_core_ribomsqc_software_versions.yml
    • Run parameters: params.json (only if -saveParams true is set)

For more details on Nextflow execution reports and troubleshooting, refer to the Nextflow documentation.
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