Lint Bactopia pipeline components against style guidelines.
Checks modules, subworkflows, and workflows for compliance with
Bactopia's GroovyDoc, structural, and configuration standards.
Usage
Required Options
| Option | Type | Default | Description |
|---|
--bactopia-path | STRING | | Directory where Bactopia repository is stored |
Scope Options
| Option | Type | Default | Description |
|---|
--modules, --no-modules | BOOL | true | Lint modules (default: on) |
--subworkflows, --no-subworkflows | BOOL | true | Lint subworkflows (default: on) |
--workflows, --no-workflows | BOOL | true | Lint workflows (default: on) |
--module | STRING | | Lint a single module by name (e.g. 'mlst', 'bakta/run') |
--subworkflow | STRING | | Lint a single subworkflow by name (e.g. 'mlst') |
--workflow | STRING | | Lint a single workflow by name (e.g. 'mlst', 'bactopia-tools/mlst') |
Output Options
| Option | Type | Default | Description |
|---|
-q, --quiet | BOOL | false | Only show components with warnings or failures |
--json | BOOL | false | Output as JSON |
--pretty | BOOL | false | Pretty-print JSON output (implies --json) |
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. |