diff --git a/src/data_processors/process_dataset/config.vsh.yaml b/src/data_processors/process_dataset/config.vsh.yaml
index 67ecba505..9184a3f8c 100644
--- a/src/data_processors/process_dataset/config.vsh.yaml
+++ b/src/data_processors/process_dataset/config.vsh.yaml
@@ -35,4 +35,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [lowcpu, highmem, hightime]
+      label: [lowcpu, midmem, hightime]
diff --git a/src/data_processors/process_dataset/script.py b/src/data_processors/process_dataset/script.py
index 4d8881434..897f59ba6 100644
--- a/src/data_processors/process_dataset/script.py
+++ b/src/data_processors/process_dataset/script.py
@@ -264,3 +264,7 @@ def subsample_adata_group_balanced(adata, group_key, n_samples, seed=0):
 
 # Save the spatial data
 sdata_output.write(par["output_sp"], overwrite=True)
+
+# Clean up zarr v2 migration temp dir only after all writes are complete
+if _tmp_dir is not None:
+    shutil.rmtree(_tmp_dir)