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review-groovydoc

Testing & Quality
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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.

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Review GroovyDoc

Run bactopia-lint focused on GroovyDoc accuracy rules and present the results.

Steps

  1. 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
    • For modules only: add --no-subworkflows --no-workflows
    • For subworkflows only: add --no-modules --no-workflows
    • For a specific module: add --module <name>

  2. Parse the JSON output. Filter results to GroovyDoc-related rules only:

    Module rules (M-series):

    • M006: GroovyDoc block present
    • M007: Required GroovyDoc tags
    • M008: @status value valid
    • M009: @tags sub-keys present
    • M010: Features list formatting
    • M014: Links use HTTPS
    • M031: @output fields match actual record() output
    • M032: @input record fields match actual input
    • M033: Optionality markers (?) match between GroovyDoc and code
    • M034: Standard fields not described in @output
    • M035: @citation keys exist in citations.yml
    • M036: GroovyDoc tag ordering
    • M037: Blank lines between GroovyDoc sections
    • M038: No */ inside GroovyDoc block

    Subworkflow rules (S-series):

    • S003: GroovyDoc with required tags
    • S004: Features comma-separated without spaces
    • S006: Links use HTTPS
    • S017: @modules match actual module includes
    • S018: @subworkflows match actual subworkflow includes
    • S019: @citation keys exist in citations.yml
    • S020: @tags complexity value is valid
    • S021: @tags input-type value is valid
    • S022: @tags output-type value is valid
    • S023: @tags features values are valid
    • S024: GroovyDoc tag ordering
    • S026: All emit channels have a corresponding @output tag
    • S027: @output field descriptions must not exist for channel.empty() emits

    Entry workflows (W-series):

    • No dedicated GroovyDoc-accuracy W-rules exist. Workflow GroovyDoc review is a manual pass — check the workflow main.nf against .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.

  3. Present results as a clean summary:

    • If all pass: Report "All X modules/subworkflows have clean GroovyDoc" and stop
    • If issues found: Group by rule ID for easy batch fixing
      • Show count of affected components per rule
      • For each rule, list the affected components and specific messages
      • Prioritize FAIL over WARN

  4. If the user asks to fix issues, apply fixes:

    Module fixes:

    • M031 (FAIL): Read the actual record() output block, update @output record(...) to match
    • M032 (FAIL): Read the actual input declaration, update @input record(...) to match
    • M033 (FAIL): Reconcile optionality markers (?) 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 ?.
    • M034 (WARN): Remove description lines for standard fields (meta, results, logs, nf_logs, versions)
    • M035 (FAIL): Check data/citations.yml for the correct key and update @citation
    • M036 (WARN): Reorder tags to match: @status -> @keywords -> @tags -> @citation -> @note -> @input -> @output
    • M037 (WARN): Add blank * lines between sections
    • M038 (FAIL): Escape or reword any */ sequence inside the GroovyDoc block (e.g. replace glob patterns like dir/*/file with an alternative wording) so the comment doesn't close prematurely

    Subworkflow fixes:

    • S017 (FAIL): Update @modules to match actual include statements (use underscore-delimited keys: blast_blastn not blastn)
    • S018 (FAIL): Update @subworkflows to match actual include statements
    • S019 (FAIL): Check data/citations.yml for the correct key and update @citation
    • S023 (FAIL): Fix invalid feature values or add missing commas
    • S024 (WARN): Reorder tags: @status -> @keywords -> @tags -> @citation -> @modules -> @subworkflows -> @note -> @input -> @output
    • S026 (FAIL): Add @output channel_name for each undocumented emit channel, with field descriptions matching the emitted record shape (see pangenome subworkflow for pattern)
    • S027 (FAIL): Move field descriptions from the channel.empty() @output to the correct @output that actually emits data

  5. After fixes, re-run the lint to confirm all issues are resolved.

Notes

  • The wrapper script auto-discovers bactopia-lint (checks PATH, then conda envs)
  • Citation keys are validated against data/citations.yml (all sections)
  • Field ordering in @output is a WARN (style), not FAIL (correctness)
  • Standard fields (meta, results, logs, nf_logs, versions) should never have description lines in @output
  • The @input should use record(meta, ...) syntax, not raw (_meta: Map, ...) syntax

GroovyDoc Quick Reference

Required Tags

Module 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

Subworkflow-Specific Tags

@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).

Optional Tags

@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)

Rules

  • No spaces after commas in features list: features:a,b,c (not features:a, b, c)
  • Standard fields (meta, results, logs, nf_logs, versions) must NOT have description lines
  • @output field list must exactly match the actual record() output block
  • @input record fields must match the actual input declaration
  • @modules/@subworkflows must match actual include statements
  • Citation keys must exist in data/citations.yml
  • Valid complexity: simple, moderate, complex
  • Valid input-type: none, single, multiple, parameter
  • Valid output-type: single, multiple