nf-core · mashehu · Oct 10, 2025 · Oct 2, 2025 · Oct 9, 2025 · Oct 9, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -30,6 +30,7 @@
 
 - Support modules with `exec:` blocks ([#3633](https://github.com/nf-core/tools/pull/3633))
 - feat: nf-core modules bump-version supports specifying the toolkit ([#3608](https://github.com/nf-core/tools/pull/3608))
+- use same logic for super-tool selection in modules lint and bump-version ([#3823](https://github.com/nf-core/tools/pull/3823))
 - Override example keywords in modules test ([#3801](https://github.com/nf-core/tools/pull/3801))
 
 ### Subworkflows

diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
@@ -116,13 +116,7 @@ def bump_versions(
                 raise nf_core.modules.modules_utils.ModuleExceptionError(
                     "You cannot specify a tool and request all tools to be bumped."
                 )
-            # First try to find an exact match
-            exact_matches = [m for m in nfcore_modules if m.component_name == module]
-            if exact_matches:
-                nfcore_modules = exact_matches
-            else:
-                # If no exact match, look for modules that start with the given name (subtools)
-                nfcore_modules = [m for m in nfcore_modules if m.component_name.startswith(module + "/")]
+            nfcore_modules = nf_core.modules.modules_utils.filter_modules_by_name(nfcore_modules, module)
 
             if len(nfcore_modules) == 0:
                 raise nf_core.modules.modules_utils.ModuleExceptionError(

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
@@ -141,7 +141,7 @@ def lint(
             if all_modules:
                 raise LintExceptionError("You cannot specify a tool and request all tools to be linted.")
             local_modules = []
-            remote_modules = [m for m in self.all_remote_components if m.component_name == module]
+            remote_modules = nf_core.modules.modules_utils.filter_modules_by_name(self.all_remote_components, module)
             if len(remote_modules) == 0:
                 raise LintExceptionError(f"Could not find the specified module: '{module}'")
         else:

diff --git a/nf_core/modules/modules_utils.py b/nf_core/modules/modules_utils.py
@@ -115,3 +115,22 @@ def load_edam():
                     if extension not in edam_formats:
                         edam_formats[extension] = (fields[0], fields[1])  # URL, name
     return edam_formats
+
+
+def filter_modules_by_name(modules: list[NFCoreComponent], module_name: str) -> list[NFCoreComponent]:
+    """
+    Filter modules by name, supporting exact matches and tool family matching.
+
+    Args:
+        modules (list[NFCoreComponent]): List of modules to filter
+        module_name (str): The module name or prefix to match
+
+    Returns:
+        list[NFCoreComponent]: List of matching modules
+    """
+    # First try to find an exact match
+    exact_matches = [m for m in modules if m.component_name == module_name]
+    if exact_matches:
+        return exact_matches
+    # If no exact match, look for modules that start with the given name (subtools)
+    return [m for m in modules if m.component_name.startswith(module_name)]
diff --git a/tests/modules/test_modules_utils.py b/tests/modules/test_modules_utils.py
@@ -18,3 +18,67 @@ def test_get_installed_modules_with_files(self):
 
         _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.nfcore_modules)
         assert len(nfcore_modules) == 1
+
+    def test_filter_modules_by_name_exact_match(self):
+        """Test filtering modules by name with an exact match"""
+        # install bpipe/test
+        _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.nfcore_modules)
+
+        # Test exact match
+        filtered = nf_core.modules.modules_utils.filter_modules_by_name(nfcore_modules, "bpipe/test")
+        assert len(filtered) == 1
+        assert filtered[0].component_name == "bpipe/test"
+
+    def test_filter_modules_by_name_tool_family(self):
+        """Test filtering modules by name to get all subtools of a super-tool"""
+        # Create some mock samtools subtools in the modules directory
+        samtools_dir = self.nfcore_modules / "modules" / "nf-core" / "samtools"
+
+        for subtool in ["view", "sort", "index"]:
+            subtool_dir = samtools_dir / subtool
+            subtool_dir.mkdir(parents=True, exist_ok=True)
+            (subtool_dir / "main.nf").touch()
+
+        # Get the modules
+        _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.nfcore_modules)
+
+        # Test filtering by tool family (super-tool)
+        filtered = nf_core.modules.modules_utils.filter_modules_by_name(nfcore_modules, "samtools")
+
+        assert set(m.component_name for m in filtered) == {"samtools/view", "samtools/sort", "samtools/index"}
+
+    def test_filter_modules_by_name_exact_match_preferred(self):
+        """Test that exact matches are preferred over prefix matches"""
+        # Create a samtools super-tool and its subtools
+        samtools_dir = self.nfcore_modules / "modules" / "nf-core" / "samtools"
+        samtools_dir.mkdir(parents=True, exist_ok=True)
+        (samtools_dir / "main.nf").touch()
+
+        # Create subtools
+        for subtool in ["view", "sort"]:
+            subtool_dir = samtools_dir / subtool
+            subtool_dir.mkdir(parents=True, exist_ok=True)
+            (subtool_dir / "main.nf").touch()
+
+        # Get the modules
+        _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.nfcore_modules)
+
+        # Test that exact match is returned when it exists
+        filtered = nf_core.modules.modules_utils.filter_modules_by_name(nfcore_modules, "samtools")
+        assert len(filtered) == 1
+        assert filtered[0].component_name == "samtools"
+
+    def test_filter_modules_by_name_no_match(self):
+        """Test filtering modules by name with no matches"""
+        _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.nfcore_modules)
+
+        # Test no match
+        filtered = nf_core.modules.modules_utils.filter_modules_by_name(nfcore_modules, "nonexistent")
+        assert len(filtered) == 0
+
+    def test_filter_modules_by_name_empty_list(self):
+        """Test filtering an empty list of modules"""
+        modules = []
+
+        filtered = nf_core.modules.modules_utils.filter_modules_by_name(modules, "fastqc")
+        assert len(filtered) == 0