diff --git a/src/depiction_targeted_preproc/pipeline/prepare_inputs.py b/src/depiction_targeted_preproc/pipeline/prepare_inputs.py
index d21c1df..4b21310 100644
--- a/src/depiction_targeted_preproc/pipeline/prepare_inputs.py
+++ b/src/depiction_targeted_preproc/pipeline/prepare_inputs.py
@@ -3,9 +3,9 @@
 from pathlib import Path
 
 import yaml
+
 from bfabric import Bfabric
 from bfabric.entities import Resource
-from bfabric.experimental.app_interface.input_preparation import prepare_folder
 
 
 def _get_ibd_resource_id(imzml_resource_id: int, client: Bfabric) -> int:
@@ -58,14 +58,3 @@ def write_inputs_spec(dataset_id: int, imzml_resource_id: int, client: Bfabric,
     inputs_yaml = sample_dir / "inputs.yml"
     with inputs_yaml.open("w") as file:
         yaml.safe_dump(inputs_spec, file)
-
-
-def prepare_inputs(
-    client: Bfabric,
-    sample_dir: Path,
-    dataset_id: int,
-    imzml_resource_id: int,
-    ssh_user: str | None,
-) -> None:
-    write_inputs_spec(dataset_id=dataset_id, imzml_resource_id=imzml_resource_id, client=client, sample_dir=sample_dir)
-    prepare_folder(inputs_yaml=sample_dir / "inputs.yml", target_folder=sample_dir, client=client, ssh_user=ssh_user)
diff --git a/src/depiction_targeted_preproc/pipeline/prepare_params.py b/src/depiction_targeted_preproc/pipeline/prepare_params.py
index b6e6174..a1d2938 100644
--- a/src/depiction_targeted_preproc/pipeline/prepare_params.py
+++ b/src/depiction_targeted_preproc/pipeline/prepare_params.py
@@ -1,13 +1,6 @@
-from pathlib import Path
-
-import cyclopts
-import yaml
-from bfabric import Bfabric
-from bfabric.entities import Workunit
-from bfabric.experimental.app_interface.workunit.definition import WorkunitExecutionDefinition
-from loguru import logger
 from pydantic import BaseModel
 
+from bfabric.experimental.app_interface.workunit.definition import WorkunitExecutionDefinition
 from depiction_targeted_preproc.pipeline_config.model import PipelineArtifact
 
 
@@ -31,44 +24,3 @@ def parse_params(definition: WorkunitExecutionDefinition) -> dict[str, str | int
         requested_artifacts=requested_artifacts,
         mass_list_id=definition.raw_parameters.get("mass_list_id"),
     ).model_dump(mode="json")
-
-
-def prepare_params(
-    client: Bfabric,
-    sample_dir: Path,
-    workunit_id: int,
-    override: bool,
-) -> None:
-    sample_dir.mkdir(parents=True, exist_ok=True)
-    params_yaml = sample_dir / "params.yml"
-    if params_yaml.is_file() and not override:
-        logger.info(f"Skipping params generation for {workunit_id} as it already exists and override is not set")
-        return
-    definition = WorkunitExecutionDefinition.from_workunit(Workunit.find(id=workunit_id, client=client))
-    with params_yaml.open("w") as file:
-        yaml.safe_dump(parse_params(definition), file)
-
-
-app = cyclopts.App()
-
-
-@app.default
-def prepare_params_from_cli(
-    sample_dir: Path,
-    config_preset: str,
-    requested_artifacts: list[str],
-    n_jobs: int = 32,
-) -> None:
-    sample_dir.mkdir(parents=True, exist_ok=True)
-    params_yaml = sample_dir / "params.yml"
-    with params_yaml.open("w") as file:
-        yaml.safe_dump(
-            Params(config_preset=config_preset, requested_artifacts=requested_artifacts, n_jobs=n_jobs).model_dump(
-                mode="json"
-            ),
-            file,
-        )
-
-
-if __name__ == "__main__":
-    app()
diff --git a/src/depiction_targeted_preproc/pipeline/store_outputs.py b/src/depiction_targeted_preproc/pipeline/store_outputs.py
deleted file mode 100644
index f8ebad8..0000000
--- a/src/depiction_targeted_preproc/pipeline/store_outputs.py
+++ /dev/null
@@ -1,36 +0,0 @@
-from __future__ import annotations
-
-from pathlib import Path
-
-import yaml
-from bfabric import Bfabric
-from bfabric.entities import Workunit
-from bfabric.experimental.app_interface.output_registration import register_outputs
-
-
-def _get_outputs_spec(zip_file_path: Path, workunit: Workunit) -> dict[str, list[dict[str, str | int | bool]]]:
-    return {
-        "outputs": [
-            {
-                "type": "bfabric_copy_resource",
-                "local_path": str(zip_file_path.absolute()),
-                "store_entry_path": zip_file_path.name,
-                "workunit_id": workunit.id,
-                "storage_id": workunit.application.storage.id,
-            }
-        ]
-    }
-
-
-def write_outputs_spec(zip_file_path: Path, workunit: Workunit) -> Path:
-    output_spec = _get_outputs_spec(zip_file_path=zip_file_path, workunit=workunit)
-    outputs_yaml = zip_file_path.parent / f"{zip_file_path.stem}_outputs_spec.yml"
-    with outputs_yaml.open("w") as file:
-        yaml.safe_dump(output_spec, file)
-    return outputs_yaml
-
-
-def store_outputs(client: Bfabric, zip_file_path: Path, workunit_id: int, ssh_user: str | None):
-    workunit = Workunit.find(id=workunit_id, client=client)
-    outputs_yaml = write_outputs_spec(zip_file_path=zip_file_path, workunit=workunit)
-    register_outputs(outputs_yaml=outputs_yaml, client=client, ssh_user=ssh_user)