nf-subworkflow-to-galaxy-workflow

Name: nf-subworkflow-to-galaxy-workflow
Availability: InStock
Author: Galaxy Project

Convert Nextflow subworkflows into reusable Galaxy workflows.

7|12|Updated Dec 17, 2025

Search Tags:#workflow #integration #pipeline #convert #Nextflow #Galaxy #subworkflow

Ready to run

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

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Converting Nextflow subworkflows into Galaxy workflows to enable reuse and integration of multi-step pipelines within Galaxy projects.

Core Features & Use Cases

Subworkflow mapping: translate a complex Nextflow subworkflow into a Galaxy workflow with step-by-step execution.
Data-flow preservation: maintain input/output connections between processes to ensure reproducibility.
Reuse & integration: enables modular components to be reused in different Galaxy contexts.

Quick Start

Install Nextflow and Galaxy locally to perform the conversion.
Identify the target subworkflow and outline its constituent processes.
Follow the step-by-step mapping described in this Skill to reconstruct the Galaxy workflow.

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

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

FAQPage Schema

How do I convert a Nextflow subworkflow into a Galaxy workflow?▼

Converting a Nextflow subworkflow into a Galaxy workflow involves identifying processes, checking tool availability, mapping data flow, building the Galaxy workflow, and validating the result to preserve input and output connections.

What is the best way to map Nextflow processes to Galaxy steps for pipeline integration?▼

The best way to map Nextflow processes to Galaxy steps is to translate multi-process subworkflows into step-by-step Galaxy executions, preserving input and output connections for reuse and integration within Galaxy projects.

Does converting Nextflow subworkflows to Galaxy preserve data flow between processes?▼

Yes, converting Nextflow subworkflows to Galaxy preserves data flow by explicitly mapping input and output connections between processes, maintaining reproducibility and ensuring correct pipeline execution.

Do I need to install Nextflow and Galaxy locally to translate Nextflow subworkflows?▼

Yes, installing Nextflow and Galaxy locally is required to perform the subworkflow conversion. This local setup allows you to identify target subworkflows and reconstruct the mapped Galaxy workflow accurately.

Can I reuse converted Nextflow subworkflows as modular components in different Galaxy contexts?▼

Yes, you can reuse converted Nextflow subworkflows as modular components in different Galaxy contexts. The translation enables modular components to be reused in different Galaxy projects for multi-step pipeline integration.

What are the limitations when translating multi-process Nextflow subworkflows to Galaxy?▼

A key limitation when translating multi-process Nextflow subworkflows is tool availability. You must check that required tools are available in Galaxy before mapping data flow and building the workflow steps.