fix review comments

nf-core · nvnieuwk · Oct 29, 2025 · Sep 26, 2025 · Sep 26, 2025 · Sep 29, 2025
commit efd1176437694ee7f16020493579055ddc14bcc8
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
@@ -295,15 +295,16 @@ def get_outputs_from_main_nf(self):
             log.debug(f"Found {len(outputs)} outputs in {self.main_nf}")
             self.outputs = outputs
 
-    def get_topics_from_main_nf(self):
+    def get_topics_from_main_nf(self) -> None:
         with open(self.main_nf) as f:
             data = f.read()
         if self.component_type == "modules":
             topics = {}
             # get topic name from main.nf after "output:". the names are always after "topic:"
             if "output:" not in data:
                 log.debug(f"Could not find any outputs in {self.main_nf}")
-                return topics
+                self.topics = topics
+                return
             output_data = data.split("output:")[1].split("when:")[0]
             regex_topic = r"topic:\s*([^)\s,]+)"
             regex_elements = r"\b(val|path|env|stdout|eval)\s*(\(([^)]+)\)|\s*([^)\s,]+))"

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
@@ -720,7 +720,7 @@ def _parse_input(self, line_raw):
     return inputs
 
 
-def _parse_output_emits(self, line):
+def _parse_output_emits(self, line:str) -> list[str]:
     output = []
     if "meta" in line:
         output.append("meta")
@@ -732,7 +732,7 @@ def _parse_output_emits(self, line):
     return output
 
 
-def _parse_output_topics(self, line):
+def _parse_output_topics(self, line:str) -> list[str]:
     output = []
     if "meta" in line:
         output.append("meta")