diff --git a/bfabric/experimental/app_interface/app_runner/__main__.py b/bfabric/experimental/app_interface/app_runner/__main__.py
new file mode 100644
index 0000000..922c217
--- /dev/null
+++ b/bfabric/experimental/app_interface/app_runner/__main__.py
@@ -0,0 +1,47 @@
+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+from typing import Union
+from venv import logger
+
+import yaml
+from pydantic import TypeAdapter, BaseModel
+
+from bfabric.bfabric import Bfabric
+from bfabric.cli_formatting import setup_script_logging
+from bfabric.experimental.app_interface.app_runner._spec import AppSpec
+from bfabric.experimental.app_interface.app_runner.runner import Runner
+
+
+class ChunksFile(BaseModel):
+    # TODO move to better location
+    chunks: list[Path]
+
+
+def main() -> None:
+    setup_script_logging()
+    client = Bfabric.from_config()
+    parser = argparse.ArgumentParser()
+    parser.add_argument("action", default="run", choices=["run"])
+    parser.add_argument("--app-spec", type=Path, required=True)
+    parser.add_argument("--workunit-ref", type=TypeAdapter(Union[int, Path]).validate_strings, required=True)
+    parser.add_argument("--work-dir", type=Path, required=True)
+    parser.add_argument("--ssh-user", type=str, required=False)
+    parser.add_argument("--read-only", action="store_true")
+    args = parser.parse_args()
+
+    app_spec = AppSpec.model_validate(yaml.safe_load(args.app_spec.read_text()))
+    runner = Runner(spec=app_spec, client=client, ssh_user=args.ssh_user)
+    runner.run_dispatch(workunit_ref=args.workunit_ref, work_dir=args.work_dir)
+    chunks_file = ChunksFile.model_validate(yaml.safe_load((args.work_dir / "chunks.yml").read_text()))
+    for chunk in chunks_file.chunks:
+        logger.info(f"Processing chunk {chunk}")
+        runner.run_prepare_input(chunk_dir=chunk)
+        runner.run_process(chunk_dir=chunk)
+        if not args.read_only:
+            runner.run_register_outputs(chunk_dir=chunk, workunit_ref=args.workunit_ref)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/bfabric/experimental/app_interface/app_runner/runner.py b/bfabric/experimental/app_interface/app_runner/runner.py
index 44897c4..a27e662 100644
--- a/bfabric/experimental/app_interface/app_runner/runner.py
+++ b/bfabric/experimental/app_interface/app_runner/runner.py
@@ -7,6 +7,7 @@
 from bfabric.experimental.app_interface.app_runner._spec import AppSpec
 from bfabric.experimental.app_interface.input_preparation import prepare_folder
 from bfabric.experimental.app_interface.output_registration import register_outputs
+from bfabric.experimental.app_interface.workunit.definition import WorkunitDefinition
 
 
 class Runner:
@@ -17,23 +18,24 @@ def __init__(self, spec: AppSpec, client: Bfabric, ssh_user: str | None = None)
 
     def run_dispatch(self, workunit_ref: int | Path, work_dir: Path) -> None:
         subprocess.run(
-            f"{self._app_spec.dispatch} {shlex.quote(str(workunit_ref))} {shlex.quote(str(work_dir))}",
+            f"{self._app_spec.commands.dispatch} {shlex.quote(str(workunit_ref))} {shlex.quote(str(work_dir))}",
             shell=True,
             check=True,
         )
 
     def run_prepare_input(self, chunk_dir: Path) -> None:
         prepare_folder(
-            inputs_yaml=chunk_dir / "inputs.yaml", target_folder=chunk_dir, client=self._client, ssh_user=self._ssh_user
+            inputs_yaml=chunk_dir / "inputs.yml", target_folder=chunk_dir, client=self._client, ssh_user=self._ssh_user
         )
 
     def run_process(self, chunk_dir: Path) -> None:
-        subprocess.run(f"{self._app_spec.process} {shlex.quote(str(chunk_dir))}", shell=True, check=True)
+        subprocess.run(f"{self._app_spec.commands.process} {shlex.quote(str(chunk_dir))}", shell=True, check=True)
 
-    def run_register_outputs(self, chunk_dir: Path, workunit_id: int) -> None:
+    def run_register_outputs(self, chunk_dir: Path, workunit_ref: int | Path) -> None:
+        workunit_definition = WorkunitDefinition.from_ref(workunit_ref, client=self._client)
         register_outputs(
-            outputs_yaml=chunk_dir / "outputs.yaml",
-            workunit_id=workunit_id,
+            outputs_yaml=chunk_dir / "outputs.yml",
+            workunit_id=workunit_definition.registration.workunit_id,
             client=self._client,
             ssh_user=self._ssh_user,
         )