metaboigniter

Orchestrate nf-core/metaboigniter runs for mass spectrometry metabolomics data processing.

1|Updated Jun 19, 2026

Search Tags:#bioinformatics #metabolomics #mass spectrometry #nf-core #nextflow #sirius #ms2query

Ready to run

npx skills add https://github.com/danilomonge/nf-claw --skill metaboigniter

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: metaboigniter
Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/metaboigniter
Command: npx skills add https://github.com/danilomonge/nf-claw --skill metaboigniter

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

It removes the manual complexity of running nf-core/metaboigniter so metabolomics researchers can process mass spectrometry data with validated parameters, reproducible outputs, and less setup risk.

Core Features & Use Cases

End-to-End Metabolomics Processing: Handles centroiding, feature detection, adduct detection, alignment, linking, and requantification for mass spectrometry-based workflows.
Identification Support: Can extend the workflow with MS2-driven identification using tools such as SIRIUS and MS2Query.
Research Use Case: Process a samplesheet of mzML files to generate standardized results, QC reports, and candidate metabolite annotations for downstream analysis.

Quick Start

Ask the skill to run metaboigniter on your samplesheet with the desired Nextflow profile and any special overrides, then write the results to your chosen output directory.

Frequently Asked Questions about metaboigniter

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I process mass spectrometry data for metabolomics using Nextflow?▼

Mass spectrometry data processing for metabolomics involves centroiding, feature detection, adduct detection, alignment, linking, and requantification to convert raw MS files into structured feature tables.

How do I run end-to-end metabolomics workflows from an mzML samplesheet?▼

Running end-to-end metabolomics workflows requires a valid CSV samplesheet of mzML files and an output directory to generate standardized results, QC reports, and candidate metabolite annotations.

Can I use SIRIUS and MS2Query for MS2-based identification in a metabolomics pipeline?▼

Yes, SIRIUS and MS2Query can extend the metabolomics pipeline to perform MS2-driven identification, generating candidate metabolite annotations for downstream analysis.

What is the best way to ensure reproducible metabolomics data processing?▼

The best way to ensure reproducible metabolomics data processing is to use schema-validated Nextflow parameters for deterministic execution, which removes manual complexity and reduces setup risk.

Do I need a specific samplesheet format for nf-core metabolomics workflows?▼

Yes, you need a valid CSV samplesheet containing your mass spectrometry data files, along with a specified output directory, to execute the workflow deterministically.