only add entry to files

Author: mirpedrol

nf_core/modules/lint/__init__.py

@@ -394,7 +394,7 @@ def update_meta_yml_file(self, mod):
                     if "ontologies" in corrected_meta_yml["input"][i][j][element_name]:
                         for ontology in corrected_meta_yml["input"][i][j][element_name]["ontologies"]:
                             current_ontologies_i.append(ontology["edam"])
-                    else:
+                    elif corrected_meta_yml["input"][i][j][element_name]["type"] == "file":
                         corrected_meta_yml["input"][i][j][element_name]["ontologies"] = []
                     log.debug(f"expected ontologies for input: {expected_ontologies_i}")
                     log.debug(f"current ontologies for input: {current_ontologies_i}")
@@ -421,7 +421,7 @@ def update_meta_yml_file(self, mod):
                     if "ontologies" in corrected_meta_yml["output"][i][ch_name][j][element_name]:
                         for ontology in corrected_meta_yml["output"][i][ch_name][j][element_name]["ontologies"]:
                             current_ontologies_o.append(ontology["edam"])
-                    else:
+                    elif corrected_meta_yml["output"][i][ch_name][j][element_name]["type"] == "file":
                         corrected_meta_yml["output"][i][ch_name][j][element_name]["ontologies"] = []
                     log.debug(f"expected ontologies for output: {expected_ontologies_o}")
                     log.debug(f"current ontologies for output: {current_ontologies_o}")