diff --git a/cadetrdm/batch_running/case.py b/cadetrdm/batch_running/case.py
index e94c1db..ffd3ee0 100644
--- a/cadetrdm/batch_running/case.py
+++ b/cadetrdm/batch_running/case.py
@@ -21,6 +21,7 @@ def __init__(
         environment: Environment| None  = None,
         name: str | None = None,
         study: Study | None = None,
+        run_method: str = "main"
      ) -> None:
         if study is not None:
             warnings.warn(
@@ -43,6 +44,7 @@ def __init__(
         self._options_hash = options.get_hash()
         self.results_branch = None
         self._current_environment = None
+        self.run_method = run_method
 
     def __str__(self):
         return self.name
@@ -213,7 +215,9 @@ def run_study(self, force=False, container_adapter: "ContainerAdapter" = None, c
                     self.status = "failed"
                     return False
             else:
-                self.project_repo.module.main(self.options, str(self.project_repo.path))
+                module = self.project_repo.module
+                run_method = getattr(module, self.run_method)
+                run_method(self.options, str(self.project_repo.path))
 
             print("Command execution successful.")
             self.status = 'finished'
diff --git a/cadetrdm/repositories.py b/cadetrdm/repositories.py
index cf1fa2a..ffd108f 100644
--- a/cadetrdm/repositories.py
+++ b/cadetrdm/repositories.py
@@ -14,6 +14,7 @@
 from stat import S_IREAD, S_IWRITE
 import tarfile
 import tempfile
+from types import ModuleType
 from typing import List, Optional, Any
 from urllib.request import urlretrieve
 
@@ -758,10 +759,19 @@ def add_list_of_remotes_in_readme_file(self, repo_identifier: str, remotes_url_l
 
 
 class ProjectRepo(BaseRepo):
-    def __init__(self, path=None, output_folder=None,
-                 search_parent_directories=True, suppress_lfs_warning=False,
-                 url=None, branch=None, options=None,
-                 *args, **kwargs):
+    def __init__(
+        self,
+        path: os.PathLike = None,
+        output_folder = None,
+        search_parent_directories: bool = True,
+        suppress_lfs_warning: bool = False,
+        url: str = None,
+        branch: str = None,
+        options: Options | None = None,
+        package_dir: str | None = None,
+         *args: Any,
+         **kwargs: Any,
+     ) -> None:
         """
         Class for Project-Repositories. Handles interaction between the project repo and
         the output (i.e. results) repo.
@@ -780,6 +790,8 @@ def __init__(self, path=None, output_folder=None,
             from a system without git-lfs
         :param branch:
             Optional branch to check out upon initialization
+        :param package_dir:
+            Name of the directory containing the main package.
         :param options:
             Options dictionary containing ...
         :param args:
@@ -823,24 +835,30 @@ def __init__(self, path=None, output_folder=None,
         if branch is not None:
             self.checkout(branch)
 
+        self._package_dir = package_dir
+
     @property
     def name(self):
         return self.path.parts[-1]
 
     @property
-    def module(self):
+    def package_dir(self) -> str:
+        if self._package_dir is None:
+            return self.name
+        return self._package_dir
+
+    @property
+    def module(self) -> ModuleType:
         cur_dir = os.getcwd()
 
-        os.chdir(self.path)
         try:
             sys.path.insert(0, str(self.path))
-            module = importlib.import_module(self.name)
+            os.chdir(self.path)
+            return importlib.import_module(self.package_dir)
         finally:
             sys.path.remove(str(self.path))
             os.chdir(cur_dir)
 
-        return module
-
     def _update_version(self, metadata, cadetrdm_version):
         current_version = Version.coerce(metadata["cadet_rdm_version"])