Merge pull request #2952 from mirpedrol/subworkflows-lint

Components: set correct sha before running component lint tests

CHANGELOG.md

@@ -22,6 +22,7 @@
 
 - Only match assignments of params in `main.nf` and not references like `params.aligner == <something>` ([#2833](https://github.com/nf-core/tools/pull/2833))
 - Include test for presence of versions in snapshot ([#2888](https://github.com/nf-core/tools/pull/2888))
+- Components: set correct sha before running component lint tests ([#2952](https://github.com/nf-core/tools/pull/2952))
 
 ### Download
 

nf_core/modules/lint/__init__.py

@@ -213,6 +213,11 @@ def lint_module(self, mod, progress_bar, registry, local=False, fix_version=Fals
 
         # Otherwise run all the lint tests
         else:
+            if self.repo_type == "pipeline" and self.modules_json:
+                # Set correct sha
+                version = self.modules_json.get_module_version(mod.component_name, mod.repo_url, mod.org)
+                mod.git_sha = version
+
             for test_name in self.lint_tests:
                 if test_name == "main_nf":
                     getattr(self, test_name)(mod, fix_version, self.registry, progress_bar)

nf_core/subworkflows/lint/__init__.py

@@ -207,6 +207,11 @@ def lint_subworkflow(self, swf, progress_bar, registry, local=False):
 
         # Otherwise run all the lint tests
         else:
+            if self.repo_type == "pipeline" and self.modules_json:
+                # Set correct sha
+                version = self.modules_json.get_subworkflow_version(swf.component_name, swf.repo_url, swf.org)
+                swf.git_sha = version
+
             for test_name in self.lint_tests:
                 getattr(self, test_name)(swf)
 

nf_core/synced_repo.py

@@ -319,9 +319,9 @@ def component_files_identical(self, component_name, base_path, commit, component
         component_dir = self.get_component_dir(component_name, component_type)
         for file in component_files:
             try:
-                files_identical[file] = filecmp.cmp(os.path.join(component_dir, file), os.path.join(base_path, file))
+                files_identical[file] = filecmp.cmp(Path(component_dir, file), Path(base_path, file))
             except FileNotFoundError:
-                log.debug(f"Could not open file: {os.path.join(component_dir, file)}")
+                log.debug(f"Could not open file: {Path(component_dir, file)}")
                 continue
         self.checkout_branch()
         return files_identical