nf-core · toniher · Mar 24, 2025 · Jan 27, 2025 · Mar 24, 2025 · Mar 24, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -48,6 +48,7 @@
 - chore(deps): update dependency textual to v2 ([#3471](https://github.com/nf-core/tools/pull/3471))
 - Install subworkflows with modules from different remotes ([#3083](https://github.com/nf-core/tools/pull/3083))
 - chore(deps): update github actions ([#3498](https://github.com/nf-core/tools/pull/3498))
+- Ontology fix comment yaml ([#3502](https://github.com/nf-core/tools/pull/3502))
 
 ## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]
 

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
@@ -422,11 +422,11 @@ def update_meta_yml_file(self, mod):
                     for ontology, ext in expected_ontologies_o:
                         if ontology not in current_ontologies_o:
                             corrected_meta_yml["output"][i][ch_name][j][element_name]["ontologies"].append(
-                                {"edam": ontology}
+                                ruamel.yaml.comments.CommentedMap({"edam": ontology})
                             )
-                            corrected_meta_yml["output"][i][ch_name][j][element_name][
-                                "ontologies"
-                            ].yaml_add_eol_comment(f"{edam_formats[ext][1]}", -1)
+                            corrected_meta_yml["output"][i][ch_name][j][element_name]["ontologies"][
+                                -1
+                            ].yaml_add_eol_comment(f"{edam_formats[ext][1]}", key="edam")
 
         # Add bio.tools identifier
         for i, tool in enumerate(corrected_meta_yml["tools"]):