Core

grid.cli

Click-based command-line interface. Entry point is grid WGS <config>.

Command-line interface for LPA KIV-CNV pipeline.

grid.cli.main()

Entry point for CLI.

grid.cli.print_banner()

Print ASCII banner.

grid.cli.print_version_and_exit(value)

grid.pipeline

Orchestrates the full WGS pipeline from a loaded config dict.

grid.pipeline.run_wgs_pipeline(console=False, config=None, **args)

grid.config

Config validation — called at pipeline startup before any steps run.

grid.config._get_nested(config, *keys)

Navigate a nested dict by key path, returning None if any key is missing.

grid.config._is_enabled(config, gate)

Return True if the config section at gate path has run=True.

grid.config.error_check_config(config, console)

grid.config.validate_steps(config, errors, warnings)

grid.config.validate_top_level(config, errors, warnings)