nf-subworkflow-to-galaxy-workflow

name	nf-subworkflow-to-galaxy-workflow
description	Convert a Nextflow subworkflow to a Galaxy workflow

Nextflow Subworkflow to Galaxy Workflow

When to Use

Use this skill when:

• Converting a Nextflow subworkflow (multiple connected processes)
• Creating a Galaxy workflow from a logical group of tools
• Building a reusable workflow component

Don't use this skill if:

• Converting a single process (use nf-process-to-galaxy-tool instead)
• Converting a complete pipeline (use nf-pipeline-to-galaxy-workflow instead)

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Step-by-Step Process

Step 1: Identify All Processes in Subworkflow

List all processes that are part of the subworkflow.

Example (CAPHEINE preprocessing):

PROCESS_VIRAL_NONRECOMBINANT subworkflow:
1. REMOVETERMINALSTOPCODON
2. SEQKIT_SPLIT
3. CAWLIGN
4. REMOVEAMBIGSEQS
5. HYPHY_CLN
6. IQTREE
7. HYPHY_LABELTREE

Step 2: Check Tool Availability for Each Process

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

cd ../
for tool in removeterminalstopcodon seqkit cawlign hyphy iqtree; do
    ./scripts/check_tool.sh $tool
done

Document results:

Process: REMOVETERMINALSTOPCODON
Tool: remove_terminal_stop_codons
Status: ✅ Found in tools-iuc
Action: Use existing tool

Process: SEQKIT_SPLIT
Tool: seqkit_split2
Status: ✅ Found in tools-iuc
Action: Use existing tool

Process: CUSTOM_PROCESS
Tool: custom_tool
Status: ❌ Not found
Action: Need to create tool → Use nf-process-to-galaxy-tool skill

Step 3: Create Missing Tools (if any)

If any tools are missing:

For each missing tool, use the nf-process-to-galaxy-tool skill to create it.

Wait for all tools to exist before continuing to Step 4.

Step 4: Map Data Flow

Identify how data flows between processes in Nextflow:

// Nextflow example
PROCESS_A(input_ch)
PROCESS_B(PROCESS_A.out.result)
PROCESS_C(PROCESS_B.out.result)

Maps to Galaxy workflow:

Step 0: Input dataset
Step 1: Tool A (input from Step 0)
Step 2: Tool B (input from Step 1 output)
Step 3: Tool C (input from Step 2 output)

See: ../workflow-to-ga.md for detailed data flow mapping

Step 5: Handle Special Patterns

Parallelization (Nextflow channels splitting):

• Use Galaxy dataset collections
• Map scatter/gather patterns

Conditionals (Nextflow when clauses):

• Use Galaxy workflow conditionals (limited)
• Or create separate workflows for different paths

Optional inputs:

• Mark as optional in workflow inputs
• Use conditional steps

See: ../workflow-to-ga.md for pattern details

Step 6: Build Workflow

Recommended approach: Use Galaxy UI

1. Open Galaxy workflow editor
2. Add input datasets
3. Add tools in order (by ToolShed ID)
4. Connect outputs to inputs
5. Configure parameters
6. Test with sample data
7. Export as .ga file

Alternative: Programmatically create .ga JSON

See: ../workflow-to-ga.md for .ga format details

Step 7: Test Workflow

Use the canonical testing docs:

• Tool testing (Planemo): ../../tool-dev/references/testing.md
• Workflow testing/validation (Galaxy instance): ../../galaxy-integration/galaxy-integration.md

../testing-and-validation.md is a short routing page that links to these.

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Quick Reference

Nextflow subworkflow = Galaxy workflow (.ga file)

Key mappings:

• Process sequence → Workflow steps
• Channel connections → Dataset connections
• Parallel processes → Dataset collections
• Conditional execution → Workflow conditionals (limited)

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Resources

All detailed guides are in parent directory (../):

• workflow-to-ga.md - Complete workflow conversion guide
• check-tool-availability.md - Tool availability checking
• nextflow-galaxy-terminology.md - Conceptual mappings
• testing-and-validation.md - Routing page to canonical testing docs

Related skills:

• nf-process-to-galaxy-tool - For creating missing tools

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Example

See ../examples/capheine-mapping.md for the PROCESS_VIRAL_NONRECOMBINANT subworkflow conversion example.

Key insight: In CAPHEINE, all tools already existed in tools-iuc, so conversion was purely workflow assembly - no tool creation needed.