Pipeline Module¶
The pipeline module orchestrates the complete VariantCentrifuge workflow.
Stage-based pipeline orchestration.
This module builds and runs the stage-based pipeline using PipelineRunner, PipelineContext, and registered Stage subclasses from pipeline_core/.
- variantcentrifuge.pipeline.check_scoring_requires_inheritance(args, config)[source]¶
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:
- variantcentrifuge.pipeline.build_pipeline_stages(args)[source]¶
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)[source]¶
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]
Notes
Config key to stage mapping (keys not listed here have no stage effect):
Config key
Stage(s) activated
scoring_config_path
VariantScoringStage
ped_file
PedigreeLoadingStage
no_stats
StatisticsGenerationStage (suppressed when True)
perform_gene_burden
GeneBurdenAnalysisStage
perform_association
AssociationAnalysisStage
xlsx
ExcelReportStage
html_report
HTMLReportStage
igv
IGVReportStage
- variantcentrifuge.pipeline.run_pipeline(args)[source]¶
Run the stage-based pipeline.
- Parameters:
args (argparse.Namespace) – Command-line arguments
- Return type: