add-subworkflow

name	add-subworkflow
description	Scaffold a new Bactopia subworkflow that orchestrates existing modules. Creates main.nf with GroovyDoc and test files. Use when asked to add a new subworkflow, create a subworkflow, or wire up modules into a subworkflow.

Add Subworkflow

Scaffold a Bactopia subworkflow that orchestrates one or more existing modules. Subworkflows are glue -- they wire modules together, aggregate results, and provide a clean interface for workflows.

Prerequisites

• The module(s) this subworkflow will use must already exist under modules/
• Read .agents/docs/standards/04-subworkflow-documentation.md for documentation standards

Interactive Questioning

This skill is interactive -- ask the user early and often, especially before creating files.

• Multiple questions at once: Use AskUserQuestion popups (up to 4 questions per batch). Mark the recommended option with "(Recommended)" at the end of its label and place it first.
• Single simple question: Just ask in chat, no popup needed.
• When in doubt: Ask. It's cheaper to clarify upfront than to regenerate files.

What a Subworkflow Contains

A subworkflow is a single main.nf file plus tests:

subworkflows/{tool}/
    main.nf              # Workflow definition with GroovyDoc
    tests/
        main.nf.test     # nf-test specification
        main.nf.test.snap # Snapshot (generated by nf-test)
        nextflow.config  # Includes ALL module.configs used by this subworkflow
        nf-test.config   # Standard nf-test config
        .nftignore       # Exclude unstable files from snapshots

No module.config or schema.json -- those belong to modules only.

Phased Workflow

Phase 1: Gather Information

Goal: Determine which modules to orchestrate and how, using interactive prompts.

Important: Use the AskUserQuestion tool for structured choices throughout this phase. Present up to 4 questions per batch. Mark the recommended option with "(Recommended)" at the end of its label and place it first in the options list.

1. Ask the user which modules this subworkflow uses. Get the module paths (e.g., modules/nohuman/run, modules/mlst).

   • Read each module's main.nf to understand its inputs and outputs.
   • Does it call other subworkflows? If so, use @subworkflows tag (not @modules) for those includes.

2. Run the lookup command if package info is needed:

   bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh lookup {package_name} --bactopia-path . --pretty
   

3. Determine the input type from the primary module's inputs, then run test-data discovery:

   bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {input_type} --bactopia-path . --pretty
   

   This returns species/accession combinations already used by similar modules, with pre-computed test_data_path, test_uncompressed_path, test_species, and test_sample_id values. Use the returned paths directly in the scaffold config (Phase 2) -- do NOT construct paths manually. Subworkflow tests use the compressed path (test_data_path).

4. Batch 1: Design choices (AskUserQuestion, up to 3 questions)

   Question 1 -- Aggregation strategy:

   • CSVTK_CONCAT -- concatenate per-sample tabular output (most common) (Recommended)
   • Dedicated summary module -- tool has its own aggregation command (rare)
   • No aggregation -- tool doesn't produce per-sample tabular output

   Question 2 -- Test data species: Present top 3-4 species from the test-data discovery results. Recommend species that exercise the tool's functionality. Include the accession in each option's description.

   Question 3 -- Aggregation field (if CSVTK_CONCAT or dedicated_summary selected): Which output field should be aggregated? (e.g., tsv, report, csv) What format? (tsv or csv)

5. Present the following for confirmation (derive from module main.nf and lookup):

---

Phase 2: File Generation

Goal: Generate the 5 subworkflow files using bactopia-scaffold.

1. Construct the JSON config from the design decisions. Write it to /tmp/scaffold-config.json:

   {
       "tool": "{tool_name}",
       "display_name": "{DisplayName}",
       "description": "{One-sentence description}",
       "process_name": "{TOOL_NAME}",
       "package": "{package_name}",
       "version": "{version}",
       "build": "{build}",
       "home_url": "{github_url}",
       "input_type": "assembly",
       "has_database": false,
       "handles_gz": false,
       "layout": "flat",
       "resource_label": "process_low"
        
        
         
        
            
            
            
       
        
                
       
        
        
            
            
            
       
        
        
        
        
   
   

---

Phase 3: Review & Customize

Goal: Review generated files and make tool-specific adjustments.

1. Subworkflow main.nf -- review and customize:

   • The @input GroovyDoc should match the subworkflow's take channel name
   • For the CSVTK_CONCAT pattern, verify the gather field and format are correct
   • If the subworkflow uses modules not in the standard pattern (e.g., calls other subworkflows), add the appropriate @subworkflows tag and adjust includes
   • The @modules tag should use underscore-delimited directory keys: csvtk_concat, {tool}

2. Test nextflow.config -- verify it includes ALL module.configs for processes in the subworkflow:

   • The primary module's config
   • csvtk/concat/module.config if using CSVTK_CONCAT
   • Any other module configs

3. Test main.nf.test -- verify:

   • Test data paths match the species/sample chosen
   • Database input lines are present if needed
   • Snapshot fields include the right output field names

4. Run the linter to catch structural issues before proceeding:

   bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-lint.sh {tool} --bactopia-path .
   

   This runs bactopia-lint scoped to the new subworkflow (and module if it exists). Fix any FAILs before moving on. Common issues:

   • S011: misaligned include braces in subworkflow
   • S019: citation key not found in data/citations.yml

5. Update data/citations.yml -- add the tool citation entry in alphabetical order (if not already present from a prior /add-module run):

   {tool}:
     name: "{ToolName}"
     link: "{github_url}"
     description: "{One-sentence description}"
     cite: "{Full citation text}"
   

6. with full paths.

---

Subworkflow Patterns

The scaffold generates one of three patterns based on the aggregation.strategy:

Strategy	Pattern	Include	Emit
csvtk_concat	CSVTK_CONCAT aggregation	gatherCsvtk from plugin	sample_outputs + run_outputs
dedicated_summary	Tool's own summary command	gatherFields from plugin	sample_outputs + run_outputs
none	No aggregation	No plugin	sample_outputs + Channel.empty()

CSVTK_CONCAT is the default and most common (~80% of subworkflows).

Edge Cases

1. Multi-module subworkflows (e.g., snippy + snpdists + gubbins): The scaffold generates a single-module pattern. For complex orchestration, generate the scaffold then manually adjust the includes and channel wiring.

2. Composite subworkflows that call other subworkflows: Add @subworkflows tag manually and adjust includes to point to ../../subworkflows/{name}/main instead of ../../modules/{name}/main.

Test Data Discovery

Test data paths are discovered dynamically from existing module tests using:

bash .agents/skills/add-bactopia-tool/scripts/run-bactopia-scaffold.sh test-data --input-type {type} --bactopia-path . --pretty

This scans modules/*/tests/main.nf.test for paths matching the input type and returns pre-computed template variables. Always use the discovered paths -- never construct test data paths manually. The output includes test_data_path (compressed, for subworkflow tests), test_uncompressed_path (for module tests), test_species, and test_sample_id.

Supported input types: assembly, reads, assembly_reads, proteins, gff, genbank.