diff --git a/snakebids/bidsapp/run.py b/snakebids/bidsapp/run.py
index 7b8179aa..894da89f 100644
--- a/snakebids/bidsapp/run.py
+++ b/snakebids/bidsapp/run.py
@@ -168,10 +168,7 @@ def build_parser(self):
         if not self._parser_built:
             self.pm.hook.initialize_config(config=self.config)
             for group in self.parser._action_groups:  # noqa: SLF001
-                if group.title is not None and group.title not in {
-                    "positional arguments",
-                    "optional arguments",
-                }:
+                if group.title is not None:
                     self.argument_groups[group.title] = group
             self.pm.hook.add_cli_arguments(
                 parser=self.parser,
diff --git a/snakebids/tests/test_bidsapp.py b/snakebids/tests/test_bidsapp.py
index a22307ac..6e2d0e1c 100644
--- a/snakebids/tests/test_bidsapp.py
+++ b/snakebids/tests/test_bidsapp.py
@@ -31,7 +31,7 @@ def add_cli_arguments(
         assert len(config) == 1
         assert config["initialized"]
         assert len(parser._actions) == 1
-        assert not argument_groups
+        assert len(argument_groups) == 2
         config["added_args"] = True
         parser.add_argument("arg_one")
         parser.add_argument("--arg-two")
@@ -192,5 +192,5 @@ def test_argument_groups_visible_to_add_arg_hook(self):
         app.parser.add_argument_group("foo")
         app.run()
         assert self.group_names
-        assert set(self.group_names) == {"foo", "new"}
+        assert set(self.group_names).issuperset({"foo", "new"})
         assert app.argument_groups["new"].title == "new"