nf-pipeline-to-galaxy-workflow

Convert Nextflow pipelines into equivalent Galaxy workflows with conversion plans.

7|12|Updated Dec 17, 2025

Search Tags:#automation #workflow #pipeline #convert #Nextflow #nf-core #Galaxy

Ready to run

npx skills add https://github.com/galaxyproject/galaxy-skills --skill nf-pipeline-to-galaxy-workflow

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Please help me install this Agent Skill.
Skill: nf-pipeline-to-galaxy-workflow
Source: https://github.com/galaxyproject/galaxy-skills/tree/main/nf-to-galaxy/nf-pipeline-to-galaxy-workflow
Command: npx skills add https://github.com/galaxyproject/galaxy-skills --skill nf-pipeline-to-galaxy-workflow

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill converts a complete Nextflow pipeline into an equivalent Galaxy workflow, enabling execution within Galaxy without rewriting pipeline logic.

Core Features & Use Cases

Full pipeline migration: maps all processes, inputs, outputs, and data flow from Nextflow to Galaxy.
Scope-aware conversion: supports whole pipelines (including nf-core patterns) and planning for subworkflows where appropriate.
Conversion planning: provides a recommended Galaxy structure (workflow components, subworkflows, and metadata) to guide implementation.

Quick Start

Provide your Nextflow project (main.nf) and optional config to begin the conversion process and obtain a Galaxy workflow plan.

Frequently Asked Questions about nf-pipeline-to-galaxy-workflow

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

FAQPage Schema

How do I convert a Nextflow pipeline to a Galaxy workflow?▼

You can convert a Nextflow pipeline to a Galaxy workflow by providing your main.nf file and optional config to generate an equivalent Galaxy workflow structure without rewriting pipeline logic.

Can I migrate nf-core pipelines to Galaxy without rewriting the logic?▼

Yes, you can migrate nf-core pipelines to Galaxy without rewriting logic. The conversion process analyzes Nextflow structures and maps all processes, inputs, and outputs directly to Galaxy components.

What does a Nextflow to Galaxy conversion plan include?▼

A Nextflow to Galaxy conversion plan includes recommended Galaxy structures such as workflow components, subworkflows, metadata, and an implementation strategy to guide the pipeline migration.

Does the conversion tool validate Nextflow processes and data flow?▼

Yes, the conversion validates the pipeline's processes, inputs, outputs, and metadata to ensure the generated Galaxy workflow accurately reflects the original Nextflow data flow.

What is the best way to handle large-scale Nextflow pipeline migrations to Galaxy?▼

For large-scale Nextflow pipeline migrations to Galaxy, the tool provides scope-aware conversion by planning subworkflows and recommending specific Galaxy tools to manage complex pipeline structures.