Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Workflow management and reproducibility

Nextflow4MS-DIAL

A reproducible Nextflow workflow for LC-HRMS metabolomics that executes MS-DIAL-based processing across local, containerized, and high-performance computing environments.

LC-MSUntargeted metabolomicsWorkflow language or engineCommand lineOpen source
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Overview

Nextflow4MS-DIAL orchestrates MS-DIAL and MS-FLO processing with Nextflow for reproducible LC-HRMS analyses. Container profiles support local and HPC execution and produce feature/annotation tables together with workflow reports.

What can this tool do?

Provenance trackingContainer supportPeak or feature detectionRetention-time alignmentSpectral-library matching

Common uses

  • Run MS-DIAL preprocessing reproducibly on local systems or HPC.
  • Preserve workflow configuration, execution logs, and containerized dependencies around an MS-DIAL analysis.

Scientific fit

Primary function

Workflow management and reproducibility

Other functions

Preprocessing and feature extraction, Metabolite annotation and identification

Analysis types

Untargeted metabolomics

MS level

MS1, MS/MS

Acquisition

Full-scan MS, Data-dependent acquisition (DDA), General or unspecified acquisition

Ion mobility

Not specified

Data compatibility

Inputs

Raw instrument data, Mass spectra, Spectral library

Outputs

Feature or peak table, Compound list or annotations, Human-readable report

Input formats

mzML, Other, ABF

Output formats

CSV or TSV

Scope and considerations

Designed for

  • Reproducible execution of MS-DIAL LC-HRMS workflows across local, container, and HPC environments.

Not designed for

  • A new standalone feature-detection algorithm or conversion of every proprietary raw format without external converters.

Important requirements

  • Nextflow, Java and Docker or Singularity in the documented Linux/macOS setup, mzML/ABF data, MS-DIAL/MS-FLO configuration files and appropriately named reference libraries.

Considerations

  • Results depend on MS-DIAL parameters and library compatibility. CPU/resource allocation and file naming must follow the workflow guidance on the chosen platform.

Access and documentation

Primary accessDocumentation

MIT workflow code; bundled or invoked programs and reference libraries retain their own terms. Use the documented execution profile and record the configuration.

License: MIT

Evidence and review

Enveda intake rechecked against official README/documentation, repository access terms and primary publication metadata on 2026-10-27. Editorial source review only; no software execution or independent benchmarking. See docs/enveda-expansion-review-2026-10-27.md.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography–Mass Spectrometry Metabolomics Data Processing. Journal of the American Society for Mass Spectrometry (2025). doi:10.1021/jasms.4c00364

Related tools

MS-DIALDepends on · A graphical and command-line workbench for untargeted metabolomics and lipidomics data processing across multiple chromatography and mass spectrometry platforms.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-10-27 · First committed entry

    Add 27 source-reviewed tools from Enveda intake

    View change · Entry at this revision

Full GitHub history