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CLI Reference

The molraptor console command exposes the molecular pipeline and metadata checks.

Help and Version

molraptor --help
molraptor run --help
molraptor --version

Run the Pipeline

Run with the default example configuration:

molraptor run

Use a custom YAML configuration:

molraptor run --config path/to/config.yaml

Enable verbose logs:

molraptor run --verbose

Run with both a custom config and verbose logging:

molraptor run --config path/to/config.yaml --verbose

Notes

  • The --config flag defaults to examples/example_config.yaml when not specified.
  • The --verbose flag sets the logger to INFO level, exposing progress messages from all molraptor.* modules. Without it, only WARNING and above are shown.