Bactopia
Official@bactopia · United States of America
Nextflow DSL2 pipeline for the complete analysis of bacterial genomes
Agent Skills by Bactopia
Showing 19 vetted skills indexed across 1 GitHub repositories.
bactopiareview-docs
Validate reference documentation against live repository state using bactopia-docs.
bactopiareview-tests
Review nf-test run results and present grouped diagnostic summaries across execution profiles.
bactopiabump-versions
Propagate versions.yml values into hand-maintained version-bearing files across the Bactopia repository.
bactopiaadd-module
Scaffolds new Bactopia Nextflow modules from bioconda packages with tests and documentation.
bactopiarelease-checklist
Audit Bactopia release readiness across repos and produce a GO or NO-GO report.
bactopiarun-tests
Runs Bactopia nf-test suites via bactopia-test and writes timestamped logs for review.
bactopiaproject-status
Reports Bactopia component counts, GroovyDoc coverage, nf-test coverage, and structural issues.
bactopiaadd-bactopia-tool
Scaffolds a complete Bactopia Tool pipeline from a bioconda package.
bactopiareview-docs
Validate .claude/docs reference documentation for staleness and drift with bactopia-docs --validate.
bactopiareview-tests
Review nf-test outputs and generate grouped error analysis summaries for bactopia runs.
bactopiareview-groovydoc
Validate GroovyDoc blocks for input/output alignment and tag ordering.
bactopiaupdate-module
Detect outdated tools in Bactopia modules and update module.config and CHANGELOG.md.
bactopiamerge-schemas
Regenerate nextflow.config and nextflow_schema.json for Bactopia workflows.
bactopiaadd-module
Scaffold Bactopia modules from Bioconda packages with standard files and tests.
bactopiareview-citations
Audit citations.yml against workflow @citation keys and report inconsistencies.
bactopiarun-tests
Run Bactopia nf-tests against target components and generate timestamped logs directories.
bactopiaproject-status
Run bactopia-status to parse JSON and summarize project health metrics.
bactopiaupdate-catalog
Regenerate Bactopia catalog.json and llms.txt via bactopia-catalog.
bactopiaadd-subworkflow
Scaffold Bactopia subworkflows with main.nf, tests, and configuration files.
Frequently Asked Questions About Bactopia
FAQPage SchemaWhat specific tasks does Bactopia enable for genomic researchers?▼
Bactopia enables the rapid scaffolding of bacterial analysis modules, sub-pipelines, and complete analysis environments. It provides standardized validation for documentation, citation integrity, and GroovyDoc alignment, while facilitating the generation of project health metrics and cataloging of genomic analysis components.
Which technical personas benefit most from these capabilities?▼
Bioinformaticians, computational biologists, and research software engineers managing large-scale bacterial genome sequencing projects benefit from these capabilities. It is designed for developers who require reproducible, modular, and well-documented genomic analysis environments built on Nextflow DSL2.
What are the prerequisites for running Bactopia components?▼
Users require a functional Nextflow environment and Bioconda access to utilize the scaffolding and module management features. The system relies on nf-test for validation and standard configuration files like module.config and nextflow_schema.json to maintain pipeline integrity.