bactopia
- 18 skills
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- 10 hours ago last updated
- ▌ Generate Skills Docs · bactopiaGenerate 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.
- ▌ Prepare Release Docs · bactopiaPrepare the Bactopia docs site for a new bactopia release. Covers the full per-release workflow: regenerating auto-generated content from the new bactopia tag, registering new Bactopia Tools in the tools index, refreshing hand-written pages for changed behavior, updating the AI Skills page, regenerating the LLM catalog, bumping the version label, snapshotting the outgoing version locally, and pushing a branch for PR review (never merging to master). Use this skill whenever a new bactopia version is released or tagged, when the user asks to update the docs for a release, bump the docs version, prepare release docs, or publish docs for a new bactopia version.
- ▌ Generate Llms Catalog · bactopiaGenerate 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.
- ▌ Run Tests · bactopia bundleRun Bactopia nf-tests via bactopia-test and produce a timestamped logs/ directory that /review-tests can interpret. Use when asked to run tests, execute tests, test a module, test a subworkflow, test a workflow, or validate a change. Accepts optional tier and component arguments (e.g., "run tests on snippy", "test abricate_run module", "test amrfinderplus subworkflow").
- ▌ Add Module · bactopiaScaffold 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.
- ▌ Review Docs · bactopia bundleReview staleness of reference docs under .agents/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 .agents/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 .agents/docs for drift after a migration.
- ▌ Review Tests · bactopia bundleReview nf-test run results and present a diagnostic summary with grouped error analysis. Use when asked to review tests, check test results, show test failures, analyze test output, investigate why tests failed, see what's broken, or check test status. Runs are multi-profile (docker/conda/singularity) with docker as the reference baseline. Accepts an optional timestamp argument to review a specific run.
- ▌ Bump Versions · bactopia bundlePropagate the Bactopia and nf-bactopia versions declared in versions.yml into the hand-maintained files that carry a literal version (conf/test_base.config, CITATION.cff, bin/bactopia, data/conda/meta.yaml). Use this whenever the user has edited versions.yml and wants the rest of the repo brought in line, or asks to bump the version, set the release version, propagate versions.yml, sync version-bearing files, fix a V001 version-consistency failure, or prepare version files for a release. This never edits versions.yml itself and never regenerates the templated artifacts (nextflow.config, catalog.json) — it hands those off to /merge-schemas and /update-catalog.
- ▌ Merge Schemas · bactopia bundleRegenerate 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.
- ▌ Update Module · bactopia bundleCheck for newer versions of tools used in Bactopia modules and apply updates to module.config files and CHANGELOG.md. Use when asked to update module versions, check for outdated tools, or bump container versions.
- ▌ Project Status · bactopia bundleShow 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.
- ▌ Update Catalog · bactopia bundleRegenerate catalog.json and llms.txt by running bactopia-catalog. Use when asked to update the catalog, rebuild the component index, refresh catalog.json, or sync llms.txt after component changes (new/removed modules, subworkflows, or workflows; tool version bumps; GroovyDoc edits that affect descriptions or contracts).
- ▌ Add Subworkflow · bactopiaScaffold 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.
- ▌ Update Datasets · bactopia bundleBuild and publish Bactopia's version-pinned datasets to Cloudflare R2. Currently implements the AMRFinder+ database. It verifies the amrfinderplus module is at the latest bioconda version, rebuilds amrfinderplus.tar.gz inside the module's pinned container, and (after confirmation) uploads it via rclone to datasets/v<version>/amrfinderplus.tar.gz. Use when asked to update datasets, rebuild the amrfinderplus database, publish a dataset bundle, refresh the version-pinned datasets, or prepare datasets for a release.
- ▌ Review Citations · bactopia bundleReview 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 Groovydoc · bactopia bundleReview 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.
- ▌ Add Bactopia Tool · bactopia bundleScaffold 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.
- ▌ Release Checklist · bactopia bundleAudit whether Bactopia is ready for a version release and produce a GO / NO-GO recommendation report. Read-only — never commits, pushes, tags, edits issues, or regenerates tracked files. Use this whenever the user asks about release readiness, cutting a release, a release checklist, whether we can ship/tag a new version, pre-release audit, or "are we ready to release" — even if they don't say the word "checklist". Covers version consistency across bactopia/bactopia-py/nf-bactopia, nf-bactopia plugin pin + template drift, module tool-version bumps, workflow config/schema and catalog freshness, docs/citations/GroovyDoc/lint validators, recent test-run status, CHANGELOG completeness, and open-issue triage.