Merge pull request nf-core#2625 from mashehu/handle-stageAs

handle stageAs in input parsing correctly
mirpedrol · Jan 4, 2024 · 1cd6bb6 · 1cd6bb6
2 parents d91a3bf + 9587aab
commit 1cd6bb6
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
@@ -170,9 +170,11 @@ def get_inputs_from_main_nf(self):
         matches = re.finditer(regex, input_data, re.MULTILINE)
         for _, match in enumerate(matches, start=1):
             if match.group(3):
-                inputs.append(match.group(3))
+                input_val = match.group(3).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
+                inputs.append(input_val)
             elif match.group(4):
-                inputs.append(match.group(4))
+                input_val = match.group(4).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
+                inputs.append(input_val)
         log.info(f"Found {len(inputs)} inputs in {self.main_nf}")
         self.inputs = inputs