refine
Run iterative refinement.
Usage
celltype-refinery refine [OPTIONS]
Options
| Option | Type | Default | Description |
|---|---|---|---|
--input | PATH | - | Input H5AD file |
--auto | FLAG | False | Enable auto policy |
--config | PATH | - | Manual config YAML |
--execute | FLAG | False | Execute refinement |
--score-threshold | FLOAT | 1.0 | Score threshold |
--min-cells | INT | 500 | Minimum cells |
--out | PATH | - | Output directory |
Examples
# Diagnostic mode
celltype-refinery refine --input annotated.h5ad --auto --out output/
# Execute mode
celltype-refinery refine --input annotated.h5ad --auto --execute --out output/
# Hybrid mode
celltype-refinery refine --input annotated.h5ad --auto --config curation.yaml --execute --out output/