nf-core · mirpedrol · Jan 7, 2025 · Jan 7, 2025 · Jan 7, 2025 · Jan 7, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,12 +8,12 @@
 
 ### Modules
 
+- Fix bump-versions: only append module name if it is a dir and contains main.nf ([#3384](https://github.com/nf-core/tools/pull/3384))
+
 ### Subworkflows
 
 ### General
 
-- bump to 3.2.0dev ([#3370](https://github.com/nf-core/tools/pull/3370))
-
 ### Version updates
 
 ## [v3.1.1 - Brass Boxfish Patch](https://github.com/nf-core/tools/releases/tag/3.1.1) - [2024-12-20]

diff --git a/nf_core/modules/modules_utils.py b/nf_core/modules/modules_utils.py
@@ -65,19 +65,20 @@ def get_installed_modules(directory: Path, repo_type="modules") -> Tuple[List[st
             local_modules = sorted([x for x in local_modules if x.endswith(".nf")])
 
     # Get nf-core modules
-    if os.path.exists(nfcore_modules_dir):
-        for m in sorted([m for m in os.listdir(nfcore_modules_dir) if not m == "lib"]):
-            if not os.path.isdir(os.path.join(nfcore_modules_dir, m)):
+    if nfcore_modules_dir.exists():
+        for m in sorted([m for m in nfcore_modules_dir.iterdir() if not m == "lib"]):
+            if not m.is_dir():
                 raise ModuleExceptionError(
                     f"File found in '{nfcore_modules_dir}': '{m}'! This directory should only contain module directories."
                 )
-            m_content = os.listdir(os.path.join(nfcore_modules_dir, m))
+            m_content = [d.name for d in m.iterdir()]
             # Not a module, but contains sub-modules
             if "main.nf" not in m_content:
                 for tool in m_content:
-                    nfcore_modules_names.append(os.path.join(m, tool))
+                    if (m / tool).is_dir() and "main.nf" in [d.name for d in (m / tool).iterdir()]:
+                        nfcore_modules_names.append(str(Path(m.name, tool)))
             else:
-                nfcore_modules_names.append(m)
+                nfcore_modules_names.append(m.name)
 
     # Make full (relative) file paths and create NFCoreComponent objects
     if local_modules_dir:

diff --git a/tests/modules/test_modules_utils.py b/tests/modules/test_modules_utils.py
@@ -0,0 +1,20 @@
+import nf_core.modules.modules_utils
+
+from ..test_modules import TestModules
+
+
+class TestModulesUtils(TestModules):
+    def test_get_installed_modules(self):
+        """Test getting installed modules"""
+        _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.nfcore_modules)
+        assert len(nfcore_modules) == 1
+        assert nfcore_modules[0].component_name == "bpipe/test"
+
+    def test_get_installed_modules_with_files(self):
+        """Test getting installed modules. When a module contains a file in its directory, it shouldn't be picked up as a tool/subtool"""
+        # Create a file in the module directory
+        with open(self.nfcore_modules / "modules" / "nf-core" / "bpipe" / "test_file.txt", "w") as fh:
+            fh.write("test")
+
+        _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.nfcore_modules)
+        assert len(nfcore_modules) == 1