only append module name if it is a dir and contains main.nf

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: