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SkillsMP 已收集 bactopia/bactopia 中的 15 个 Skill。打开任一 Skill 可查看来源和详情。
已展示 15 / 15 个已收集 Skill。
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…
原文语言：英语
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…
原文语言：英语
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.
原文语言：英语
Propagate 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…
原文语言：英语
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.
原文语言：英语
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.
原文语言：英语
Audit 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…
原文语言：英语
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…
原文语言：英语
Review 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…
原文语言：英语
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,…
原文语言：英语
Review 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…
原文语言：英语
Run 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…
原文语言：英语
Regenerate 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…
原文语言：英语
Build 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,…
原文语言：英语
Check 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.
原文语言：英语