From 2d2be3877fe04dbc4ddb80cf525be0db13083740 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Wed, 24 Jul 2024 16:03:33 +0200
Subject: [PATCH] fix typing and linting

---
 nf_core/components/nfcore_component.py | 11 +++++------
 nf_core/subworkflows/lint/__init__.py  | 21 ++++++++++++++-------
 nf_core/subworkflows/lint/meta_yml.py  |  1 +
 3 files changed, 20 insertions(+), 13 deletions(-)

diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index db817db905..39a4ba51f4 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -158,7 +158,7 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st
 
     def get_inputs_from_main_nf(self) -> None:
         """Collect all inputs from the main.nf file."""
-        inputs = []
+        inputs: list[list | str] = []
         with open(self.main_nf) as f:
             data = f.read()
         if self.component_type == "modules":
@@ -173,10 +173,10 @@ def get_inputs_from_main_nf(self) -> None:
             # don't match anything inside comments or after "output:"
             if "input:" not in data:
                 log.debug(f"Could not find any inputs in {self.main_nf}")
-                return inputs
+                return
             input_data = data.split("input:")[1].split("output:")[0]
             for line in input_data.split("\n"):
-                channel_elements = []
+                channel_elements: list[dict] = []
                 regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
                 matches = re.finditer(regex, line)
                 for _, match in enumerate(matches, start=1):
@@ -195,15 +195,14 @@ def get_inputs_from_main_nf(self) -> None:
             # get input values from main.nf after "take:"
             if "take:" not in data:
                 log.debug(f"Could not find any inputs in {self.main_nf}")
-                return inputs
+                return
             # get all lines between "take" and "main" or "emit"
             input_data = data.split("take:")[1].split("main:")[0].split("emit:")[0]
             for line in input_data.split("\n"):
                 try:
                     inputs.append(line.split()[0])
                 except IndexError:
-                    # Empty lines
-                    pass
+                    pass  # Empty lines
             log.debug(f"Found {len(inputs)} inputs in {self.main_nf}")
             self.inputs = inputs
 
diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py
index e0911e5bd9..22025d2a07 100644
--- a/nf_core/subworkflows/lint/__init__.py
+++ b/nf_core/subworkflows/lint/__init__.py
@@ -231,7 +231,6 @@ def lint_subworkflow(self, swf, progress_bar, registry, local=False):
 
             self.failed += [LintResult(swf, *s) for s in swf.failed]
 
-
     def update_meta_yml_file(self, swf):
         """
         Update the meta.yml file with the correct inputs and outputs
@@ -251,9 +250,13 @@ def update_meta_yml_file(self, swf):
         # Compare inputs and add them if missing
         if "input" in meta_yaml:
             # Delete inputs from meta.yml which are not present in main.nf
-            meta_yaml_corrected["input"] = [input for input in meta_yaml["input"] if list(input.keys())[0] in swf.inputs]
+            meta_yaml_corrected["input"] = [
+                input for input in meta_yaml["input"] if list(input.keys())[0] in swf.inputs
+            ]
             # Obtain inputs from main.nf missing in meta.yml
-            inputs_correct = [list(input.keys())[0] for input in meta_yaml_corrected["input"] if list(input.keys())[0] in swf.inputs]
+            inputs_correct = [
+                list(input.keys())[0] for input in meta_yaml_corrected["input"] if list(input.keys())[0] in swf.inputs
+            ]
             inputs_missing = [input for input in swf.inputs if input not in inputs_correct]
             # Add missing inputs to meta.yml
             for missing_input in inputs_missing:
@@ -261,9 +264,15 @@ def update_meta_yml_file(self, swf):
 
         if "output" in meta_yaml:
             # Delete outputs from meta.yml which are not present in main.nf
-            meta_yaml_corrected["output"] = [output for output in meta_yaml["output"] if list(output.keys())[0] in swf.outputs]
+            meta_yaml_corrected["output"] = [
+                output for output in meta_yaml["output"] if list(output.keys())[0] in swf.outputs
+            ]
             # Obtain output from main.nf missing in meta.yml
-            outputs_correct = [list(output.keys())[0] for output in meta_yaml_corrected["output"] if list(output.keys())[0] in swf.outputs]
+            outputs_correct = [
+                list(output.keys())[0]
+                for output in meta_yaml_corrected["output"]
+                if list(output.keys())[0] in swf.outputs
+            ]
             outputs_missing = [output for output in swf.outputs if output not in outputs_correct]
             # Add missing inputs to meta.yml
             for missing_output in outputs_missing:
@@ -274,5 +283,3 @@ def update_meta_yml_file(self, swf):
             log.info(f"Updating {swf.meta_yml}")
             yaml.dump(meta_yaml_corrected, fh)
             run_prettier_on_file(fh.name)
-
-
diff --git a/nf_core/subworkflows/lint/meta_yml.py b/nf_core/subworkflows/lint/meta_yml.py
index 633061e247..be282bc453 100644
--- a/nf_core/subworkflows/lint/meta_yml.py
+++ b/nf_core/subworkflows/lint/meta_yml.py
@@ -9,6 +9,7 @@
 
 log = logging.getLogger(__name__)
 
+
 def meta_yml(subworkflow_lint_object, subworkflow):
     """
     Lint a ``meta.yml`` file