only add entry to files

nf-core · Feb 20, 2025 · 3da314b · 3da314b
1 parent 2edbe25
commit 3da314b
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/nf_core/modules/lint/__init__.py b/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}")