By bactopia

Scaffold a complete Bactopia Tool across all three tiers -- module, subworkflow, and workflow entry point under workflows/bactopia-tools/.

bactopia/bactopia

Propagate the Bactopia and nf-bactopia versions declared in versions.yml into the hand-maintained files that carry a literal version (conf/testbase.config, CITATION.cff, bin/bactopia…

bactopia/bactopia

Regenerate nextflow.config and nextflowschema.json for Bactopia workflows by running bactopia-merge-schemas.

bactopia/bactopia

Show a live snapshot of the Bactopia project state — component counts, GroovyDoc coverage, nf-test coverage, and structural issues.

bactopia/bactopia

Audit whether Bactopia is ready for a version release and produce a GO / NO-GO recommendation report.

bactopia/bactopia

Review citation integrity across data/citations.yml and @citation tags using bactopia-citations --validate.

bactopia/bactopia

Review staleness of reference docs under .agents/docs/ using bactopia-docs --validate.

bactopia/bactopia

Review GroovyDoc accuracy across modules and subworkflows using bactopia-lint.

bactopia/bactopia

Review nf-test run results and present a diagnostic summary with grouped error analysis.

bactopia/bactopia

Regenerate catalog.json and llms.txt by running bactopia-catalog.

bactopia/bactopia

Build and publish Bactopia's version-pinned datasets to Cloudflare R2.

bactopia/bactopia

Check for newer versions of tools used in Bactopia modules and apply updates to module.config files and CHANGELOG.md.

bactopia/bactopia

Run Bactopia nf-tests via bactopia-test and produce a timestamped logs/ directory that /review-tests can interpret.

bactopia/bactopia

Scaffold a new Bactopia module from a bioconda/conda-forge package.

bactopia/bactopia

Scaffold a new Bactopia subworkflow that orchestrates existing modules.

bactopia/bactopia