nf-process-to-galaxy-tool

Convert a Nextflow process into a Galaxy tool XML wrapper.

7|12|Updated Dec 17, 2025

Search Tags:#bioinformatics #conversion #Nextflow #tool-wrapping #workflow-porting #tool-XML #Galaxy

Ready to run

npx skills add https://github.com/galaxyproject/galaxy-skills --skill nf-process-to-galaxy-tool

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This skill provides a practical path to convert an individual Nextflow process into a Galaxy tool XML wrapper, enabling rapid porting of workflows to Galaxy.

Core Features & Use Cases

Convert a single Nextflow process into a Galaxy tool XML wrapper for reusable integration.
Extract inputs, outputs, and command mappings from the process and generate a compliant tool description.
Use during pipeline porting when a specific tool wrapper is missing or when validating a tool before release.

Quick Start

Use the conversion workflow on a Nextflow process to generate the corresponding Galaxy tool XML, then validate it with Galaxy tooling.

Frequently Asked Questions about nf-process-to-galaxy-tool

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

FAQPage Schema

How do I convert a Nextflow process to a Galaxy tool XML wrapper?▼

Porting Nextflow pipelines to Galaxy involves converting each individual Nextflow process into a standalone Galaxy tool XML wrapper. You extract the process inputs and outputs to generate a compliant tool description for reusable workflow integration.

Can I wrap a specific bioinformatics tool for Galaxy using my existing Nextflow process?▼

Yes, you can wrap a specific bioinformatics tool for Galaxy by extracting the command mappings and input definitions from your Nextflow process. The conversion generates a standard tool XML wrapper ready for integration into your Galaxy workflow.

What is the best way to validate a generated Galaxy tool XML from a Nextflow process?▼

The best way to validate a generated Galaxy tool XML is by using standard Galaxy tooling after the conversion. This ensures the extracted Nextflow process inputs, outputs, and command mappings produce a compliant and functional tool description before release.

When do I need to generate a Galaxy tool XML from a Nextflow process?▼

You need to generate a Galaxy tool XML from a Nextflow process during pipeline porting when a specific tool wrapper is missing or when validating a tool before release. It enables rapid wrapping of individual bioinformatics processes for Galaxy integration.

Does converting Nextflow processes to Galaxy XML support entire workflows or single processes?▼

Converting Nextflow processes to Galaxy XML targets individual single processes rather than entire workflows. You extract inputs, outputs, and commands from one process to generate a compliant Galaxy tool XML wrapper for reusable integration.