Merge pull request #3156 from nvnieuwk/fix/tool-subtool-same-name

Fix issue where tool and subtool have the same name

nf_core/components/nfcore_component.py

@@ -64,12 +64,15 @@ def __init__(
             self.process_name = ""
             self.environment_yml: Optional[Path] = Path(self.component_dir, "environment.yml")
 
-            name_index = (
-                len(self.component_dir.parts)
-                - 1
-                - self.component_dir.parts[::-1].index(self.component_name.split("/")[0])
-            )
+            component_list = self.component_name.split("/")
+
+            name_index = len(self.component_dir.parts) - 1 - self.component_dir.parts[::-1].index(component_list[0])
+            if len(component_list) != 1 and component_list[0] == component_list[1]:
+                # Handle cases where the subtool has the same name as the tool
+                name_index -= 1
+
             repo_dir = self.component_dir.parts[:name_index][-1]
+
             self.org = repo_dir
             self.nftest_testdir = Path(self.component_dir, "tests")
             self.nftest_main_nf = Path(self.nftest_testdir, "main.nf.test")

tests/modules/test_lint.py

@@ -186,6 +186,15 @@ def test_modules_lint_trimgalore(self):
         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")
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
+        module_lint.lint(print_results=False, module="tabix/tabix")
+        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_empty(self):
         """Test linting a pipeline with no modules installed"""
         self.mods_remove.remove("fastqc", force=True)