Nf Process To Galaxy Tool

Nextflow Process to Galaxy Tool

When to Use

Use this skill when:

• Converting a single Nextflow process to a Galaxy tool
• Creating a Galaxy tool wrapper for a specific bioinformatics tool
• You've identified a missing tool during pipeline conversion

Don't use this skill if:

• The tool already exists in Galaxy (check first with ../check-tool-availability.md)
• You're converting a whole workflow (use nf-subworkflow-to-galaxy-workflow instead)

Step-by-Step Process

Step 1: Check if Tool Already Exists

CRITICAL: Always check first.

Use: ../check-tool-availability.md and ../scripts/check_tool.sh

cd ../
./scripts/check_tool.sh TOOL_NAME

If tool exists: Stop here, use existing tool. You don't need this skill.

If tool doesn't exist: Continue to Step 2.

Step 2: Decide Where to Create Tool

Use: ../tool-sources.md for decision guidance

Options:

1. tools-iuc (if community-useful and you have access)
2. Custom tool (if project-specific)

Present decision to user and wait for approval.

If targeting tools-iuc, follow the higher-level tool creation guidance in:

• ../../tool-dev/SKILL.md

Step 3: Extract Process Information

Identify from Nextflow process:

• Container image
• Input files/parameters
• Output files
• Command/script

See: ../process-to-tool.md for detailed extraction guide

Step 4: Map to Galaxy Tool XML

Use these references:

• ../container-mapping.md - Container → bioconda package
• ../datatype-mapping.md - File patterns → Galaxy datatypes
• ../process-to-tool.md - Complete mapping guide

Step 5: Create Tool XML

Follow Galaxy tool XML structure:

• <tool> wrapper
• <requirements> (from container)
• <command> (from script)
• <inputs> (from process inputs)
• <outputs> (from process outputs)
• <tests> (create test cases)
• <help> (documentation)

See: ../process-to-tool.md for complete examples

Step 6: Validate

planemo lint tool.xml
planemo test tool.xml

Quick Reference

One Nextflow process = One Galaxy tool XML

Key mappings:

• container → <requirements> (bioconda package)
• input: path(file) → <param type="data" format="..."/>
• output: path("*.ext") → <data format="..." name="output"/>
• script: """...""" → <command><![CDATA[...]]></command>

Resources

These docs live in the parent directory (../):

• process-to-tool.md - Complete process-to-tool conversion guide
• check-tool-availability.md - Tool availability checking
• tool-sources.md - Where to create tools
• container-mapping.md - Container to bioconda mapping
• datatype-mapping.md - File patterns to Galaxy datatypes
• testing-and-validation.md - Routing page to canonical testing docs
• ../../tool-dev/references/testing.md - Tool testing with Planemo

Example

See ../examples/capheine-mapping.md for real-world examples of process analysis.

Note: CAPHEINE shows a case where all tools already existed, so no tool creation was needed. This is common - always check first!