Nextflow to Galaxy Conversion (Router)

Purpose

This is a router skill that directs you to the appropriate specialized skill based on what you're converting.

For complete pipelines, you are expected to include bioinformatics best-practice sanity checks and discuss QC + reporting requirements (e.g. MultiQC). See

nf-pipeline-to-galaxy-workflow/SKILL.md

What Are You Converting?

Option 1: Single Nextflow Process → Galaxy Tool

Converting: One Nextflow process to one Galaxy tool XML

Example:

HYPHY_FEL

hyphy_fel.xml

Use skill:

nf-process-to-galaxy-tool

When to use:

• Creating a Galaxy tool wrapper for a specific bioinformatics tool
• You've identified a missing tool during pipeline conversion
• Converting a single nf-core module

Option 2: Nextflow Subworkflow → Galaxy Workflow

Converting: Multiple connected Nextflow processes to a Galaxy workflow

Example:

PROCESS_VIRAL_NONRECOMBINANT

.ga

Use skill:

nf-subworkflow-to-galaxy-workflow

When to use:

• Converting a logical group of processes
• Building a reusable workflow component
• Most processes already have Galaxy tools

Option 3: Complete Nextflow Pipeline → Galaxy Solution

Converting: Full Nextflow pipeline to complete Galaxy solution

Example:

CAPHEINE

Use skill:

nf-pipeline-to-galaxy-workflow

When to use:

• Converting an nf-core pipeline
• Large-scale conversion project
• Need to plan tool creation + workflow assembly

Key Concepts

Before using any sub-skill, understand these mappings:

.nf

.ga

<requirements>

Critical: One Nextflow process = One Galaxy tool

Read:

nextflow-galaxy-terminology.md

Getting Started

New to this skill? See

README.md

Using Galaxy integration? See

../../galaxy-integration/README.md

../../galaxy-integration/galaxy-integration.md

Shared Resources

Core Guides

• ../../galaxy-integration/galaxy-integration.md

  - Galaxy MCP/BioBlend: setup, tool checking, workflow testing

• check-tool-availability.md

  - Manual tool checking across repositories

• testing-and-validation.md

  - Routing page to canonical testing docs

• ../../tool-dev/references/testing.md

  - Tool testing with Planemo

Tool Discovery Order (Installed vs Available vs Missing)

Before you conclude a tool is "missing", distinguish:

1. Installed on your target Galaxy instance (ready to use in a

   .ga

   ).
2. Not installed, but has an existing wrapper that can be installed (ToolShed / tools-iuc / known maintainers).
3. No wrapper exists (tool wrapper must be created).

If you determine (3) applies, use

nf-process-to-galaxy-tool/

When a tool is not installed on the target instance, follow the repository search order in

check-tool-availability.md

Common ToolShed owners to check (not exhaustive):

• iuc

• devteam

• bgruening

• genouest

Reference Documentation

• nextflow-galaxy-terminology.md

  - Concept mappings (process→tool, workflow→.ga)

• process-to-tool.md

  - Process → Tool conversion details

• workflow-to-ga.md

  - Workflow → .ga conversion details

• container-mapping.md

  - Container → Conda package mapping

• datatype-mapping.md

  - File patterns → Galaxy datatypes

• tool-sources.md

  - Where to create tools (tools-iuc vs custom)

Scripts & Examples

• scripts/

  - Automation scripts (see

  scripts/README.md

  )

• examples/

  - Complete conversion examples (see

  examples/README.md

  )

Quick Decision Tree

What are you converting?
│
├─ Single process?
│  └─ Use: nf-process-to-galaxy-tool
│
├─ Subworkflow (multiple processes)?
│  └─ Use: nf-subworkflow-to-galaxy-workflow
│
└─ Complete pipeline?
   └─ Use: nf-pipeline-to-galaxy-workflow

Sub-Skills

nf-process-to-galaxy-tool/

Convert a single Nextflow process to a Galaxy tool XML.

nf-subworkflow-to-galaxy-workflow/

Convert a Nextflow subworkflow to a Galaxy workflow.

nf-pipeline-to-galaxy-workflow/

Convert a complete Nextflow pipeline to a Galaxy solution.