AI Skills
These 12 skills automate common Bactopia development tasks through AI-assisted
coding tools. Each skill wraps one or more
bactopia-py CLI commands with interactive guidance,
guardrails, and multi-step orchestration. Skills live in the bactopia repo at
.claude/skills/ and are invoked with /skill-name.
Overview
| Skill | Category | Description |
|---|---|---|
/add-bactopia-tool | Scaffolding | Scaffold a complete Bactopia Tool across all three tiers -- module, subworkflow, and workflow. |
/add-module | Scaffolding | Scaffold a new Bactopia module from a bioconda/conda-forge package. |
/add-subworkflow | Scaffolding | Scaffold a new Bactopia subworkflow that orchestrates existing modules. |
/merge-schemas | Maintenance | Regenerate nextflow.config and nextflow_schema.json for Bactopia workflows. |
/update-catalog | Maintenance | Regenerate catalog.json and llms.txt. |
/update-module | Maintenance | Check for newer versions of tools used in Bactopia modules and apply updates. |
/review-groovydoc | Review & Quality | Review GroovyDoc accuracy across modules and subworkflows. |
/review-citations | Review & Quality | Review citation integrity across data/citations.yml and @citation tags. |
/review-docs | Review & Quality | Review staleness of reference docs under .claude/docs/. |
/review-tests | Review & Quality | Review nf-test run results with grouped error analysis. |
/run-tests | Testing | Run Bactopia nf-tests and produce a timestamped logs directory. |
/project-status | Project | Show a live snapshot of project state, coverage, and structural issues. |
Scaffolding
Skills that create new Bactopia components from bioconda/conda-forge packages.
/add-bactopia-tool
Scaffold a complete Bactopia Tool pipeline from a bioconda/conda-forge package, creating all three tiers (module, subworkflow, workflow) in one shot.
Wraps: bactopia-scaffold
When to use:
- Add a new analysis tool to Bactopia Tools from a bioconda package
- Create all three tiers (module, subworkflow, workflow) in one shot
- Prefer this over
/add-moduleor/add-subworkflowwhen the goal is a complete tool
Examples:
/add-bactopia-tool fastp
/add-bactopia-tool checkm2
Related skills: /add-module, /add-subworkflow,
/run-tests, /update-catalog
/add-module
Scaffold a complete Bactopia module for a bioconda/conda-forge package, creating all required files with GroovyDoc documentation and nf-test tests.
Wraps: bactopia-scaffold
When to use:
- Add a new module without the full bactopia-tool scaffolding
- Create module files (main.nf, module.config, schema.json, tests)
- Scaffold just the process layer for a tool
Examples:
/add-module snippy
/add-module fastqc
Related skills: /add-bactopia-tool, /add-subworkflow
/add-subworkflow
Scaffold a Bactopia subworkflow that orchestrates one or more existing modules. Subworkflows wire modules together, aggregate results, and provide a clean interface for workflows.
Wraps: bactopia-scaffold
When to use:
- Create a subworkflow to orchestrate existing modules
- Wire up modules into a reusable analysis unit
- Add the glue layer between modules and workflows
Examples:
/add-subworkflow snippy
/add-subworkflow amrfinderplus
Related skills: /add-bactopia-tool, /add-module
Maintenance
Skills that keep existing components up to date.
/merge-schemas
Regenerate the nextflow.config and nextflow_schema.json files for one or more
Bactopia workflows. Auto-discovers each workflow's output directory from
catalog.json so the caller never hand-computes paths.
Wraps: bactopia-merge-schemas
When to use:
- Sync workflow configs after module schema changes
- Rebuild nextflow_schema.json for a specific workflow
- Regenerate configs after adding or modifying parameters
Examples:
/merge-schemas teton
/merge-schemas teton and staphopia
/merge-schemas all tools
Related skills: /update-module, /update-catalog
/update-catalog
Regenerate the machine-readable Bactopia component index (catalog.json) and the
AI-discovery surface (llms.txt).
Wraps: bactopia-catalog
When to use:
- Sync catalog.json after adding or removing components
- Refresh llms.txt after GroovyDoc edits that affect descriptions
- Update the component index after tool version bumps
Examples:
/update-catalog
Related skills: /project-status, /merge-schemas
/update-module
Check for newer versions of bioconda tools used in Bactopia modules and apply updates to module.config files.
Wraps: bactopia-update
When to use:
- Check if any modules have outdated tool versions
- Bump container versions to the latest bioconda release
- Update a specific module's tool version
Examples:
/update-module
/update-module snippy
Related skills: /merge-schemas, /project-status
Review & Quality
Skills that audit documentation, citations, and code quality.
/review-groovydoc
Run bactopia-lint focused on GroovyDoc accuracy rules. Checks @output/@input field matching, @modules/@subworkflows lists, citation keys, tag ordering, and formatting.
Wraps: bactopia-lint
When to use:
- Validate documentation accuracy across modules and subworkflows
- Check @output/@input fields match actual channel declarations
- Audit GroovyDoc after editing module or subworkflow docs
Examples:
/review-groovydoc
/review-groovydoc snippy
Related skills: /review-citations, /review-docs
/review-citations
Run bactopia-citations --validate and present the integrity report. Detects
orphan citation keys (defined but never referenced) and workflow @citation keys
that don't resolve to a citations.yml entry.
Wraps: bactopia-citations
When to use:
- Audit citations.yml for orphan or missing entries
- Validate that workflow @citation tags resolve correctly
- Clean up unused citations after removing tools
Examples:
/review-citations
Related skills: /review-groovydoc, /review-docs
/review-docs
Run bactopia-docs --validate and present the staleness report. Detects
deprecated patterns and ground-truth violations (stale counts, wrong Nextflow
version, references to nonexistent commands or lint rule IDs).
Wraps: bactopia-docs
When to use:
- Check reference docs for outdated information after migrations
- Verify doc claims match current repo state
- Scan .claude/docs for drift after adding or removing components
Examples:
/review-docs
Related skills: /review-groovydoc, /review-citations,
/project-status
/review-tests
Review nf-test run results and present a diagnostic summary with grouped error analysis.
Wraps: bactopia-review-tests
When to use:
- Analyze test output after running
/run-tests - Investigate why tests failed with grouped error summaries
- Review a specific test run by timestamp
Examples:
/review-tests
/review-tests 20260324_081306
Related skills: /run-tests
Testing
/run-tests
Run the Bactopia nf-test suite through bactopia-test for a specific component
and produce a timestamped logs/ directory that /review-tests can interpret.
Wraps: bactopia-test
When to use:
- Run tests for a specific module, subworkflow, or workflow
- Validate changes before committing
- Generate test snapshots for newly scaffolded components
Examples:
/run-tests snippy
/run-tests abricate module
/run-tests amrfinderplus subworkflow
Related skills: /review-tests
Project
/project-status
Show a live snapshot of the Bactopia project state -- component counts, GroovyDoc coverage, nf-test coverage, and structural issues.
Wraps: bactopia-status
When to use:
- Check overall project state and coverage metrics
- Find components missing documentation or tests
- Get a quick summary of what needs attention
Examples:
/project-status
Related skills: /update-catalog, /run-tests