Merge pull request #218 from ArcInstitute/216-unable-to-specify-negative-control-name-in-data-preprocessing

216 unable to specify negative control name in data preprocessing

Author: noamteyssier

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cell-eval"
-version = "0.6.7"
+version = "0.6.8"
 description = "Evaluation metrics for single-cell perturbation predictions"
 readme = "README.md"
 authors = [

src/cell_eval/_cli/_prep.py

@@ -280,6 +280,9 @@ def run_prep(args: ap.Namespace):
         else args.input.replace(".h5ad", ".prep.vcc"),
         pert_col=args.pert_col,
         celltype_col=args.celltype_col,
+        output_pert_col=args.output_pert_col,
+        output_celltype_col=args.output_celltype_col,
+        ntc_name=args.ntc_name,
         encoding=args.encoding,
         allow_discrete=args.allow_discrete,
         exp_gene_dim=args.expected_gene_dim if args.expected_gene_dim != -1 else None,