// 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.
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 when asked to add a new bactopia tool, create a bactopia tool, scaffold a complete tool, add a new analysis tool to bactopia-tools, or wire up a bioconda package as a bactopia-tool. This skill handles the full pipeline from package lookup through file generation -- do not use add-module or add-subworkflow separately when the goal is a complete bactopia-tool.
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 module.
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.
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.
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 whenever the user asks to review citations, check citation integrity, audit citations.yml, find orphan citations, clean up unused citations, validate workflow @citation tags, or verify that every tool cited in a workflow has a matching entry in the citations file.
Review staleness of reference docs under .claude/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 module/subworkflow/workflow counts, wrong Nextflow version, references to nonexistent bactopia-* commands or lint rule IDs, skill-inventory drift between 06-skills.md and .claude/skills/, broken markdown link targets). Use this skill whenever the user asks to review docs, check doc staleness, audit reference docs, find outdated documentation, verify doc claims, check if docs are current, or scan .claude/docs for drift after a migration.
| name | project-status |
| description | 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. |
Run the status script and interpret the output for the user.
Run bactopia-status via the wrapper script:
bash .claude/skills/project-status/scripts/run-bactopia-status.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --json
Parse the JSON output and present a clean, readable summary. Lead with:
Highlight the most important gaps — prioritize by:
If the user asks "what should I work on next?", suggest the highest-priority gaps from the output.
bactopia-status (checks PATH, then conda envs)nftest.root_test)timestamp — when the report was generatedrepo — path to the Bactopia repositorygit — branch, commit, modified file countcounts — modules, subworkflows, workflowstiers — per-tier detail, each with total, doc_count, issues[], tag_coverage
tag_coverage — map of tag name to count of components that have itnftest — total (workflow count), tested, root_testAll components use these required tags:
@status — stable, beta, or deprecated@keywords — comma-separated search terms@tags — complexity:<simple|moderate|complex> input-type:<single|multiple|parameter> output-type:<single|multiple> features:<list>@citation — comma-separated bibtex keys@note — optional caveats or requirementsModules and subworkflows also use:
@input — input channel descriptions (can be multi-line for records)@output — output channel descriptions (single-line)Subworkflows additionally use:
@subworkflows — list of included subworkflows (directory keys)@modules — list of included modules (directory keys)Entry workflows use:
@subworkflows — included subworkflows (directory keys); workflows never call modules directly, so @modules is not used@input — parameter inputs (e.g., rundir)@section — groups published outputs@publish — file patterns with descriptions (within sections)@note — can appear at top level or within a sectionmodule.config, schema.jsonmain.nfmain.nf