Adjust moscot parameters for memory efficiency

Author: LouisK92

src/methods_cell_type_annotation/moscot/config.vsh.yaml

@@ -28,12 +28,12 @@ arguments:
     required: false
     direction: input
     type: double
-    default: 1.0
+    default: 0.3
   - name: --rank
     required: false
     direction: input
     type: integer
-    default: 5000
+    default: 500 #5000
   - name: --mapping_mode
     required: false
     direction: input

src/methods_cell_type_annotation/moscot/script.py

@@ -39,8 +39,8 @@
    'celltype_key': 'cell_type',
    'alpha': 0.8,
    'epsilon': 0.01,
-   'tau': 1.0,
-   'rank': 5000,
+   'tau': 0.3,
+   'rank': 500, #5000
    'mapping_mode': 'max',
 }
 meta = {
@@ -61,6 +61,8 @@
 if adata_sp.n_obs < 10000:
     print('Adjusting rank to -1 since data set is small (n_obs < 10k)', flush=True)
     par['rank'] = -1
+    print("Also, adjusting tau to 1.0 since data set is small", flush=True)
+    par['tau'] = 1.0
 
 # Check for normalized layer and centroid information
 assert "normalized" in adata_sc.layers.keys(), 'Layer "normalized" is required for single-cell anndata'