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SkillsMP는 bactopia/bactopia에서 15개의 skill을 수집했습니다. skill을 열어 소스와 세부 정보를 확인하세요.
수집된 skill 15개 중 15개를 표시합니다.
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…
원문 언어: 영어
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…
원문 언어: 영어
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.
원문 언어: 영어
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…
원문 언어: 영어
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.
원문 언어: 영어
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.
원문 언어: 영어
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…
원문 언어: 영어
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…
원문 언어: 영어
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…
원문 언어: 영어
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,…
원문 언어: 영어
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…
원문 언어: 영어
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…
원문 언어: 영어
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…
원문 언어: 영어
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,…
원문 언어: 영어
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.
원문 언어: 영어