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 process → hyphy_fel.xml tool

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 subworkflow → Galaxy .ga workflow

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 pipeline → Multiple Galaxy workflows + any missing tools

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:

Critical: One Nextflow process = One Galaxy tool

Read: nextflow-galaxy-terminology.md for detailed conceptual mapping

Getting Started

New to this skill? See README.md for file organization and navigation.

Using Galaxy integration? See ../../galaxy-integration/README.md and ../../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/shared/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/ to create a Galaxy tool wrapper.

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.