Audit citations.yml against workflow @citation keys and report inconsistencies.
npx skills add https://github.com/bactopia/bactopia --skill review-citations
Please help me install this Agent Skill. Skill: review-citations Source: https://github.com/bactopia/bactopia/tree/main/.claude/skills/review-citations Command: npx skills add https://github.com/bactopia/bactopia --skill review-citations
This skill validates and audits citation usage across Bactopia's citations.yml and workflow @citation tags, identifying orphan keys and workflow references that do not resolve, and helping maintain provenance-consistent metadata.
Run bactopia-citations --validate to generate the integrity report.
High-intent search queries and answers about installing and using this skill.
You can audit citation keys by running bactopia-citations --validate to generate an integrity report. This report compares your data/citations.yml file against workflow @citation tags to identify orphan keys, missing references, and provenance-only entries.
Orphan citation keys in a citations.yml file occur when metadata entries are defined but never referenced by any workflow @citation tag. Auditing tools detect these unreferenced entries to help maintain provenance-consistent metadata and guide clean removals.
Finding missing workflow citation references requires a validation tool that flags @citation keys not mapped to an entry in citations.yml. The bactopia-citations wrapper produces a JSON report detailing these missing keys to surface unresolved references in complex citation graphs.
Yes, the bactopia-citations validation wrapper requires conda, python3, and the bactopia-citations package to operate. These dependencies are necessary to parse complex citation graphs and emit the automated JSON payload for integrity auditing.
Yes, a citation audit can surface provenance_only entries for informational purposes and future wiring. The validation process identifies these entries to help you track metadata that exists for provenance but lacks active workflow references.
Fixing unresolved workflow @citation tags involves applying recommended wire-ups or clean removals based on the audit report. The validation output guides you through resolving orphan keys and missing references to maintain provenance-consistent metadata.
bactopiaScaffolds a complete Bactopia Tool pipeline from a bioconda package.
rauffataliVerify and repair BibTeX citation metadata with DOI, arXiv, and URL validation.
bactopiaRun bactopia-status to parse JSON and summarize project health metrics.
shandleyCross-check inline citations against bibliographies to identify missing or orphan references.
