bactopia-citations
Print or validate citations used throughout Bactopia.
Default mode prints the full citation list (or one entry with --name). Pass --validate to instead scan the repo for orphan keys (defined but never referenced) and workflow @citation keys that don't resolve to an entry in citations.yml. Module and subworkflow @citation keys are validated by bactopia-lint (rules M035 and S019).
Usage
bactopia-citations [OPTIONS]
Required Options
| Option | Type | Default | Description |
|---|---|---|---|
--bactopia-path, -b | STRING | Directory where Bactopia repository is stored |
Output Options
| Option | Type | Default | Description |
|---|---|---|---|
--name, -n | STRING | Only print citation matching a given name | |
--plain-text, -p | BOOL | false | Disable rich formatting |
--validate | BOOL | false | Validate citation integrity: orphan keys + workflow @citation references |
--json | BOOL | false | Emit validation results as JSON (use with --validate) |
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. |