Improve integration merging script

modules/local/merge_integrations.nf

@@ -11,15 +11,21 @@ process MERGE_INTEGRATIONS {
   """
   #!/usr/bin/python3
   import scanpy as sc
+  import anndata as ad
 
   adata = sc.read_h5ad("${original_adata}")
 
   for integration_name, integration_adata_path in zip(["${integration_names.join("\",\"")}"], ["${integration_adatas.join("\",\"")}"]):
-      integration_adata = sc.read_h5ad(integration_adata_path)
+      integration_adata = ad.read_h5ad(integration_adata_path, backed='r')
       column_name = 'X_' + integration_name
-      adata.obsm[column_name] = integration_adata.obsm[column_name]
+      adata.obsm[column_name] = integration_adata.obsm[column_name].copy()
       del integration_adata
 
+      print("Merged integration: " + integration_name)
+      print("Object now looks like:")
+      print(adata)
+      print("")
+
   adata.write('integrations.h5ad')
   """
 }