Fix/4447 linting supressed

nf_core/components/nfcore_component.py

@@ -278,8 +278,10 @@ def _extract_value(self, text: str, start_pos: int = 0, split_on_comma: bool = F
     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]'
-        with open(self.main_nf) as f:
-            data = f.read()
+        data = ""
+        if self.main_nf.is_file():
+            with open(self.main_nf) as f:
+                data = f.read()
         if self.component_type == "modules":
             # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo
             # regex matches:
@@ -323,8 +325,10 @@ def get_inputs_from_main_nf(self) -> None:
             self.inputs = inputs
 
     def get_outputs_from_main_nf(self):
-        with open(self.main_nf) as f:
-            data = f.read()
+        data = ""
+        if self.main_nf.is_file():
+            with open(self.main_nf) as f:
+                data = f.read()
         if self.component_type == "modules":
             outputs = {}
             # get output values from main.nf after "output:". the names are always after "emit:"
@@ -366,8 +370,10 @@ def get_outputs_from_main_nf(self):
             self.outputs = outputs
 
     def get_topics_from_main_nf(self) -> None:
-        with open(self.main_nf) as f:
-            data = f.read()
+        data = ""
+        if self.main_nf.is_file():
+            with open(self.main_nf) as f:
+                data = f.read()
         if self.component_type == "modules":
             topics: dict[str, list[dict[str, dict] | list[dict[str, dict[str, str]]]]] = {}
             # get topic name from main.nf after "output:". the names are always after "topic:"

nf_core/modules/lint/__init__.py

@@ -331,7 +331,11 @@ def update_meta_yml_file(self, mod):
         """
         Update the meta.yml file with the correct inputs, outputs, topics and containers
         """
-        meta_yml = self.read_meta_yml_patched(mod)
+        try:
+            meta_yml = self.read_meta_yml_patched(mod)
+        except LookupError:
+            log.warning(f"Could not reverse-apply patch to read meta.yml for {mod.component_name}, skipping update")
+            return
         if meta_yml is None:
             log.warning(f"Could not read meta.yml for {mod.component_name}, skipping update")
             return

nf_core/modules/lint/environment_yml.py

@@ -141,7 +141,15 @@ def lint_environment_yml(
         # Parse the YAML content
         env_yml = yaml.load(content)
         if env_yml is None:
-            raise ruamel.yaml.scanner.ScannerError("Empty YAML file")
+            module.failed.append(
+                (
+                    "environment_yml",
+                    "environment_yml_exists",
+                    "Module's `environment.yml` is empty",
+                    module.environment_yml,
+                )
+            )
+            return
 
         module.passed.append(
             (