Pipelines

All Immunology analysis pipelines run in backend-analysis and are dispatched asynchronously.

List live definitions and parameter schemas:

curl http://localhost:8001/immunology/pipelines

Pipeline index

Pipeline	Endpoint	Outputs
immune_composition	POST /immunology/run/immune-composition	Population counts, proportions, group summaries
immune_annotation	POST /immunology/run/immune-annotation	Immune labels, state programs, cell preview
repertoire_analysis	POST /immunology/run/repertoire-analysis	Clonotypes, diversity, V/J usage, expansion, overlap
cell_communication	POST /immunology/run/cell-communication	Ligand-receptor interactions, pathways, cytokine networks, deltas
disease_workflows	POST /immunology/run/disease-workflows	Trajectory, spatial niche, TLS, proximity, cohort summaries
multimodal_profiling	POST /immunology/run/multimodal-profiling	ADT, ATAC, multiome, cytometry summaries
interpret	POST /immunology/run/interpret	Grounded interpretation JSON with citations and audit artifacts
report	POST /immunology/run/report	Report JSON, methods text, tables, figure specs, provenance

Polling

GET /immunology/jobs/{run_id}

Versioning

Every run records platform_version and the submitted parameter JSON. Use run IDs, pipeline names, versions, and artifact paths in methods sections.

Shared engines

Immunology is the canonical owner for:

• repertoire_analysis
• cell_communication

Oncology imports these shared engines instead of duplicating the logic.