bactopia

Scaffold a complete Bactopia Tool across all three tiers -- module, subworkflow, and workflow entry point under workflows/bactopia-tools/. Creates all files (main.nf, module.config, schema.json, nextflow.config, tests) for the common single-tool pattern. Use when asked to add a new bactopia tool, create a bactopia tool, scaffold a complete tool, add a new analysis tool to bactopia-tools, or wire up a bioconda package as a bactopia-tool. This skill handles the full pipeline from package lookup through file generation -- do not use add-module or add-subworkflow separately when the goal is a complete bactopia-tool.

Scaffold a new Bactopia module from a bioconda/conda-forge package. Creates main.nf, module.config, schema.json, and test files following project standards. Use when asked to add a new module, create a new module, scaffold module files, or add a new tool's module.

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.

Regenerate nextflow.config and nextflow_schema.json for Bactopia workflows by running bactopia-merge-schemas. Use when asked to merge schemas, regenerate workflow config, rebuild nextflow_schema.json, or sync workflow configs after module schema changes.

Show a live snapshot of the Bactopia project state — component counts, GroovyDoc coverage, nf-test coverage, and structural issues. Use when asked about project state, coverage, what's missing, what's documented, or what needs attention.

Review citation integrity across data/citations.yml and @citation tags using bactopia-citations --validate. Detects orphan citation keys (defined in the yml but never referenced) and workflow @citation keys that don't resolve to a yml entry. Use this skill whenever the user asks to review citations, check citation integrity, audit citations.yml, find orphan citations, clean up unused citations, validate workflow @citation tags, or verify that every tool cited in a workflow has a matching entry in the citations file.

Review staleness of reference docs under .claude/docs/ using bactopia-docs --validate. Detects deprecated patterns (residue from past migrations like flattenPaths, the 4-channel emission framing, meta:Map) and ground-truth violations (stale module/subworkflow/workflow counts, wrong Nextflow version, references to nonexistent bactopia-* commands or lint rule IDs, skill-inventory drift between 06-skills.md and .claude/skills/, broken markdown link targets). Use this skill whenever the user asks to review docs, check doc staleness, audit reference docs, find outdated documentation, verify doc claims, check if docs are current, or scan .claude/docs for drift after a migration.

Review GroovyDoc accuracy across modules and subworkflows using bactopia-lint. Checks @output/@input field matching, @modules/@subworkflows lists, citation keys, tag ordering, and formatting. Use when asked to review GroovyDoc, check documentation accuracy, validate module/subworkflow docs, or audit GroovyDoc.

Generate llms.txt and catalog.json files for LLM consumption from the Bactopia docs site content. Run this skill whenever documentation content is added, removed, or updated, when the user asks to regenerate the LLM catalog, refresh llms.txt, update the LLM index, or sync the static LLM files with the current documentation.

Generate the AI Skills reference page for the Bactopia docs site. Runs a Python parser to extract structured metadata from the bactopia repo's SKILL.md files, then generates developers/ai-skills/index.mdx with an overview table and per-skill entries. Use this skill whenever skills are added, removed, or updated in the bactopia repo, when the user asks to regenerate the skills docs page, refresh the skills reference, update the AI skills documentation, or sync the docs site with the current set of bactopia skills.

Regenerate catalog.json and llms.txt in the bactopia-py repo root by introspecting pyproject.toml entry points and CLI modules. Use this skill whenever the user asks to update the catalog, refresh catalog.json, sync llms.txt, or after adding/removing/renaming CLI commands. Also use when the user mentions that catalog.json or llms.txt is out of date, stale, or drifted from the actual commands.