// 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, validate module/subworkflow docs, or audit GroovyDoc.
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.
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.
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.
| name | review-groovydoc |
| description | 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, validate module/subworkflow docs, or audit GroovyDoc. |
Run bactopia-lint focused on GroovyDoc accuracy rules and present the results.
Run bactopia-lint via the wrapper script. By default, lint both modules and subworkflows:
bash .claude/skills/review-groovydoc/scripts/run-bactopia-lint.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --quiet --json --silent
--no-subworkflows --no-workflows--no-modules --no-workflows--module <name>Parse the JSON output. Filter results to GroovyDoc-related rules only:
Module rules (M-series):
*/ inside GroovyDoc blockSubworkflow rules (S-series):
Entry workflows (W-series):
.claude/docs/standards/06-workflow-documentation.md, verify @subworkflows directory keys match actual include { ... } imports (e.g., utils_bactopia-tools, bactopia_qc), validate @citation keys against data/citations.yml, confirm @input names match declared params { }, and ensure each @section has ≥1 @publish. The one-off drift-check approach used on 2026-04-10 lived at /tmp/workflow_drift_check.py and reused parse_groovydoc_full() + parse_includes() from bactopia-py/bactopia/nf.py.Present results as a clean summary:
If the user asks to fix issues, apply fixes:
Module fixes:
record() output block, update @output record(...) to match@input record(...) to match?) between GroovyDoc and code. If the doc field has ? but the code doesn't, either add optional: true / Path? to the code or drop the ? from the doc. If the code is optional but the doc isn't, add the ?.data/citations.yml for the correct key and update @citation* lines between sections*/ sequence inside the GroovyDoc block (e.g. replace glob patterns like dir/*/file with an alternative wording) so the comment doesn't close prematurelySubworkflow fixes:
@modules to match actual include statements (use underscore-delimited keys: blast_blastn not blastn)@subworkflows to match actual include statementsdata/citations.yml for the correct key and update @citation@output channel_name for each undocumented emit channel, with field descriptions matching the emitted record shape (see pangenome subworkflow for pattern)channel.empty() @output to the correct @output that actually emits dataAfter fixes, re-run the lint to confirm all issues are resolved.
bactopia-lint (checks PATH, then conda envs)data/citations.yml (all sections)@input should use record(meta, ...) syntax, not raw (_meta: Map, ...) syntaxModule order: @status -> @keywords -> @tags -> @citation -> @note -> @input -> @output Subworkflow order: @status -> @keywords -> @tags -> @citation -> @modules -> @subworkflows -> @note -> @input -> @output
@status stable|beta|deprecated
@keywords comma, separated, keywords
@tags complexity:<level> input-type:<type> output-type:<type> features:<list>
@citation comma, separated, bibtex_keys
@modules bactopia_gather, csvtk_concat
@subworkflows scrubber, nohuman
Module names use underscore-delimited keys matching directory structure: blast_blastn (not blastn), bactopia_qc (not qc).
@note Title
Description text
@input record(meta, field1, field2)
- `meta`: Groovy Record containing sample information
- `field1`: Description
@input param_name
Description of non-record parameter
@output record(meta, field1, results, logs, nf_logs, versions)
- `field1`: Description (tool-specific fields only)
features:a,b,c (not features:a, b, c)record() output blockdata/citations.yml