snakemake-interface-common

import os from dataclasses import dataclass, field from snakemake_interface_common.settings import CommonSettingsBase @dataclass class MyPluginCommonSettings(CommonSettingsBase): """ A hypothetical plugin's common settings inheriting from CommonSettingsBase. This demonstrates how shared configuration parameters for a Snakemake plugin are defined using the interface. """ my_plugin_param: str = field( default="default_plugin_value", metadata={ "help": "A common setting for MyPlugin." } ) # Example of a sensitive setting, typically loaded from an environment variable api_key: str = field( default=os.environ.get("MYPLUGIN_API_KEY", ""), metadata={ "help": "API key for MyPlugin service (from MYPLUGIN_API_KEY env var).", "env_var": "MYPLUGIN_API_KEY", "sensitive": True, }, ) # Instantiate the settings. In a real Snakemake plugin, these would be populated # from command-line arguments or Snakemake profiles. settings = MyPluginCommonSettings(my_plugin_param="custom_value_from_profile_or_cli") print(f"My plugin parameter: {settings.my_plugin_param}") if settings.api_key: print("API Key loaded (value not shown for security).") else: print("MYPLUGIN_API_KEY environment variable not set.") # This class is primarily for defining structure; direct executable quickstarts # are more relevant for full Snakemake plugins.