Detailed contracts are split by decision point so the agent only loads the material needed for the current stage.
| File | Use it for |
|---|---|
input-contract.md |
Versioned configuration, sample-sheet and h5ad requirements, count validation, identifiers, reference consistency, contrast and confounding checks. |
scientific-workflow.md |
Per-sample QC, Scrublet, preserved representations, optional Harmony, resolution sweep, clustering and descriptive markers. |
annotation-contract.md |
Marker-panel evidence, conflicts, reference compatibility, Unknown, and user-confirmed mappings. |
statistics-contract.md |
Donor-aware pseudobulk DE, pairing, explicit design formulas, replication gates and Milo DA. |
output-contract.md |
Checkpoints, resume invalidation, structured statuses, report, manifest, checksums and Artifact registration. |
README_zh.md |
Chinese directory guide with the same structure as this file. |
These documents describe scientific and execution contracts, not biological ground truth or a substitute for study-specific review.