Merge pull request #3535 from toniher/fix-output-detection-in-lint-3513

adding boundary in regex for fixing #3513

Author: toniher

CHANGELOG.md

@@ -60,6 +60,7 @@
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.11.2 ([#3521](https://github.com/nf-core/tools/pull/3521))
 - Fix indentation in included_configs API docs ([#3523](https://github.com/nf-core/tools/pull/3523))
 - chore(deps): update python:3.12-slim docker digest to a866731 ([#3527](https://github.com/nf-core/tools/pull/3527))
+- adding boundary in regex ([#3535](https://github.com/nf-core/tools/pull/3535))
 - switch to using runsOn runners in nf-core/tools repo ([#3537](https://github.com/nf-core/tools/pull/3537))
 
 ## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]

nf_core/components/nfcore_component.py

@@ -207,7 +207,7 @@ def get_inputs_from_main_nf(self) -> None:
             for line in input_data.split("\n"):
                 channel_elements: Any = []
                 line = line.split("//")[0]  # remove any trailing comments
-                regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
+                regex = r"\b(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
                 matches = re.finditer(regex, line)
                 for _, match in enumerate(matches, start=1):
                     input_val = None
@@ -247,7 +247,7 @@ def get_outputs_from_main_nf(self):
                 return outputs
             output_data = data.split("output:")[1].split("when:")[0]
             regex_emit = r"emit:\s*([^)\s,]+)"
-            regex_elements = r"(val|path|env|stdout)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
+            regex_elements = r"\b(val|path|env|stdout)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
             for line in output_data.split("\n"):
                 match_emit = re.search(regex_emit, line)
                 matches_elements = re.finditer(regex_elements, line)