capellini.pipeline

Top-level pipeline orchestrator.

Classes

CapelliniPipeline(config)

Run the CAPELLINI pipeline stages in order, sharing inter-stage state.

class capellini.pipeline.CapelliniPipeline(config: CapelliniConfig)

Bases: object

Run the CAPELLINI pipeline stages in order, sharing inter-stage state.

STAGE_LABELS = {'dada2': 'DADA2', 'ncbi_mapping': '3-layer NCBI ID Mapping', 'network': 'Enhanced Networks Estimation', 'preflight': 'Preflight', 'procs': 'Protein Clusters (ProCs) Estimation', 'spacepharer': 'SpacePHARER Execution'}

STAGE_ORDER = ['preflight', 'dada2', 'ncbi_mapping', 'spacepharer', 'procs', 'network']

run_all() → None

Run every stage in STAGE_ORDER.

run_from(name: str) → None

Run from the given stage to the end.

run_stage(name: str) → Any

Dispatch a single stage by name.