Pipeline Module

The pipeline module orchestrates the complete VariantCentrifuge workflow.

Refactored pipeline using the new Stage architecture.

This module demonstrates how to use the refactored pipeline stages to replace the monolithic pipeline.py functionality.

variantcentrifuge.pipeline.check_scoring_requires_inheritance(args, config)

Check if scoring configuration requires inheritance analysis.

Parameters:

• args (argparse.Namespace) – Command-line arguments

• config (dict) – Configuration dictionary

Returns:

True if inheritance analysis is required for scoring

Return type:

bool

variantcentrifuge.pipeline.build_pipeline_stages(args)

Build the list of stages based on configuration.

Parameters:

args (argparse.Namespace) – Command-line arguments

Returns:

List of stages to execute

Return type:

List[Stage]

variantcentrifuge.pipeline.create_stages_from_config(config)

Create pipeline stages from a configuration dictionary.

This function is used by CLI handlers that need to create stages without full argparse.Namespace objects.

Parameters:

config (dict) – Configuration dictionary with pipeline settings

Returns:

List of stages for the current configuration

Return type:

List[Stage]

variantcentrifuge.pipeline.run_refactored_pipeline(args)

Run the refactored pipeline with the new architecture.

Parameters:

args (argparse.Namespace) – Command-line arguments

Return type:

None

variantcentrifuge.pipeline.main()

Show example main function demonstrating how to use the refactored pipeline.