bactopia-docs
Validate reference-doc staleness across a Bactopia repo.
Two checks run against every .md file under [b]--docs-path[/b]:
[b]Deprecated patterns (D0xx)[/b]: regex matches against
[b]--patterns-file[/b] entries — phrases retired by past migrations
(e.g. flattenPaths, the 4-channel emission framing).
[b]Ground-truth assertions (D1xx)[/b]: counts (D101-D103), Nextflow version (D104), bactopia-py CLI references (D105), lint rule IDs (D106), markdown link targets (D108).
Suppress a rule on a single line with
<!-- bactopia-docs: ignore D0xx --> (or a comma-separated list).
Exits 1 if any FAIL is found.
Usage
bactopia-docs [OPTIONS]
Required Options
| Option | Type | Default | Description |
|---|---|---|---|
--bactopia-path, -b | STRING | Directory where Bactopia repository is stored |
Validation Options
| Option | Type | Default | Description |
|---|---|---|---|
--docs-path | STRING | .claude/docs | Docs directory relative to --bactopia-path |
--patterns-file | STRING | data/docs-patterns.yml | Deprecated-patterns YAML relative to --bactopia-path |
--bactopia-py-path | PATH | Path to bactopia-py repo (for D105 CLI / D106 lint-rule checks). Defaults to <bactopia-path>/../bactopia-py | |
--skip-path-check | BOOL | false | Skip D108 markdown-link target resolution |
--validate | BOOL | false | Run validation (default action; flag is accepted for parity with bactopia-citations) |
Output Options
| Option | Type | Default | Description |
|---|---|---|---|
--json | BOOL | false | Emit results as JSON |
--plain-text, -p | BOOL | false | Disable rich formatting |
Additional Options
| Option | Type | Default | Description |
|---|---|---|---|
--verbose | BOOL | false | Print debug related text |
--silent | BOOL | false | Only critical errors will be printed |
--version, -V | BOOL | false | Show the version and exit. |