Merge pull request #3541 from toniher/addressing-3530

Linting: Addressing more cases than can happen when processing input and output values

Author: mirpedrol

CHANGELOG.md

@@ -23,6 +23,7 @@
 - Fix default linting of nf-core components when `nf-core pipelines lint` is ran ([#3480](https://github.com/nf-core/tools/pull/3480))
 - Fix the unexpected warning and sychronize the `README.md` and `RO-crate-metadata.json` ([#3493](https://github.com/nf-core/tools/pull/3493))
 - Adapt the linter to the new notation used to include the centralized nf-core configs ([#3491](https://github.com/nf-core/tools/pull/3491))
+- Addressing more cases than can happen when processing input and output values ([#3541](https://github.com/nf-core/tools/pull/3541))
 
 ### Modules
 

nf_core/components/nfcore_component.py

@@ -216,8 +216,10 @@ def get_inputs_from_main_nf(self) -> None:
                     elif match.group(4):
                         input_val = match.group(4).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
                     if input_val:
-                        input_val = re.sub(r"\s*\,\s*arity\s*\:\s*\w+\s*", "", input_val).strip()  # remove arity
-                        input_val = input_val.strip("'").strip('"')  # remove quotes
+                        input_val = re.split(r',(?=(?:[^\'"]*[\'"][^\'"]*[\'"])*[^\'"]*$)', input_val)[
+                            0
+                        ]  # Takes only first part, avoid commas in quotes
+                        input_val = input_val.strip().strip("'").strip('"')  # remove quotes and whitespaces
                         channel_elements.append({input_val: {}})
                 if len(channel_elements) > 0:
                     inputs.append(channel_elements)
@@ -263,8 +265,10 @@ def get_outputs_from_main_nf(self):
                     elif match_element.group(4):
                         output_val = match_element.group(4)
                     if output_val:
-                        output_val = re.sub(r"\s*\,\s*arity\s*\:\s*\w+\s*", "", output_val).strip()  # remove arity
-                        output_val = output_val.strip("'").strip('"')  # remove quotes
+                        output_val = re.split(r',(?=(?:[^\'"]*[\'"][^\'"]*[\'"])*[^\'"]*$)', output_val)[
+                            0
+                        ]  # Takes only first part, avoid commas in quotes
+                        output_val = output_val.strip().strip("'").strip('"')  # remove quotes and whitespaces
                         output_channel[match_emit.group(1)].append({output_val: {}})
                 outputs.append(output_channel)
             log.debug(f"Found {len(outputs)} outputs in {self.main_nf}")

tests/modules/test_lint.py

@@ -187,6 +187,15 @@ def test_modules_lint_trimgalore(self):
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
 
+    def test_modules_lint_trinity(self):
+        """Test linting the Trinity module"""
+        self.mods_install.install("trinity")
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
+        module_lint.lint(print_results=False, module="trinity")
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
     def test_modules_lint_tabix_tabix(self):
         """Test linting the tabix/tabix module"""
         self.mods_install.install("tabix/tabix")