Merge pull request #3317 from lmReef/fix-linting-error

Fix meta_yml linting error

CHANGELOG.md

@@ -25,6 +25,7 @@
 ### Linting
 
 - allow mixed `str` and `dict` entries in lint config ([#3228](https://github.com/nf-core/tools/pull/3228))
+- fix meta_yml linting test failing due to module.process_name always being "" ([#3317](https://github.com/nf-core/tools/pull/3317))
 - fix module section regex matching wrong things ([#3321](https://github.com/nf-core/tools/pull/3321))
 
 ### Modules

nf_core/components/nfcore_component.py

@@ -62,7 +62,6 @@ def __init__(
             # Initialize the important files
             self.main_nf: Path = Path(self.component_dir, "main.nf")
             self.meta_yml: Optional[Path] = Path(self.component_dir, "meta.yml")
-            self.process_name = ""
             self.environment_yml: Optional[Path] = Path(self.component_dir, "environment.yml")
 
             component_list = self.component_name.split("/")
@@ -96,6 +95,8 @@ def __init__(
             self.test_yml = None
             self.test_main_nf = None
 
+        self.process_name: str = self._get_process_name()
+
     def __repr__(self) -> str:
         return f"<NFCoreComponent {self.component_name} {self.component_dir} {self.repo_url}>"
 
@@ -169,6 +170,13 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st
                         included_components.append(component)
         return included_components
 
+    def _get_process_name(self):
+        with open(self.main_nf) as fh:
+            for line in fh:
+                if re.search(r"^\s*process\s*\w*\s*{", line):
+                    return re.search(r"^\s*process\s*(\w*)\s*{.*", line).group(1) or ""
+        return ""
+
     def get_inputs_from_main_nf(self) -> None:
         """Collect all inputs from the main.nf file."""
         inputs: Any = []  # Can be 'list[list[dict[str, dict[str, str]]]]' or 'list[str]'

nf_core/modules/lint/main_nf.py

@@ -256,7 +256,6 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
     bioconda_packages = []
 
     # Process name should be all capital letters
-    self.process_name = lines[0].split()[1]
     if all(x.upper() for x in self.process_name):
         self.passed.append(("process_capitals", "Process name is in capital letters", self.main_nf))
     else: