diff --git a/src/depiction_targeted_preproc/example/.gitignore b/src/depiction_targeted_preproc/example/.gitignore
deleted file mode 100644
index 6f4740b..0000000
--- a/src/depiction_targeted_preproc/example/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-data-raw
-data-work
-data-output
diff --git a/src/depiction_targeted_preproc/example/__init__.py b/src/depiction_targeted_preproc/example/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/src/depiction_targeted_preproc/example/run.py b/src/depiction_targeted_preproc/example/run.py
deleted file mode 100644
index 5a54cce..0000000
--- a/src/depiction_targeted_preproc/example/run.py
+++ /dev/null
@@ -1,69 +0,0 @@
-import shutil
-from pathlib import Path
-
-import yaml
-from depiction_targeted_preproc.pipeline.setup import initial_setup
-from depiction_targeted_preproc.pipeline_config.artifacts_mapping import ARTIFACT_FILES_MAPPING
-from depiction_targeted_preproc.pipeline_config.artifacts_mapping import get_result_files
-from depiction_targeted_preproc.pipeline_config.model import PipelineParameters, PipelineArtifact
-from depiction_targeted_preproc.workflow.snakemake_invoke import SnakemakeInvoke
-from loguru import logger
-
-
-def main() -> None:
-    dir_raw = Path(__file__).parent / "data-raw"
-    dir_work = Path(__file__).parent / "data-work"
-    dir_output = Path(__file__).parent / "data-output"
-    dir_work.mkdir(exist_ok=True, parents=True)
-    dir_output.mkdir(exist_ok=True, parents=True)
-    # sample_name = "menzha_20231208_s607930_64074-b20-30928-a"
-    # sample_name = "menzha_20231210_s607943_64005-b20-47740-g"
-    # sample_name = "menzha_20231208_s607923_tonsil-repro-sample-01"
-    sample_name = "menzha_20231208_s607923_tonsil-repro-sample-01-findmf"
-    # sample_name = "menzha_20231208_s607923_tonsil-repro-sample-01_mcc"
-    # sample_name = "menzha_20231208_s607923_tonsil-repro-sample-01_peptnoise"
-    # sample_name = "antdit_20240606_mbrain_20um"
-    # sample_name = "20240606_mbrain_20um_timstof"
-
-    params_file = Path(__file__).parents[1] / "pipeline_config" / "default.yml"
-    params = PipelineParameters.model_validate(yaml.safe_load(params_file.read_text()))
-    logger.info("Pipeline parameters: {params}", params=params.dict())
-
-    if not (dir_work / sample_name / "raw.imzML").exists():
-        initial_setup(
-            input_imzml=dir_raw / f"{sample_name}.imzML",
-            # input_mass_list=dir_raw / "mass_list_vend.csv",
-            input_mass_list=dir_raw / "Dataset_50020.csv",
-            params_file=params_file,
-            dir=dir_work / sample_name,
-        )
-
-    result_files = get_result_files(params, dir_work, sample_name)
-    SnakemakeInvoke().invoke(work_dir=dir_work, result_files=result_files)
-    export_results(
-        work_dir=dir_work,
-        output_dir=dir_output,
-        sample_name=sample_name,
-        requested_artifacts=params.requested_artifacts,
-        result_file_mapping=ARTIFACT_FILES_MAPPING,
-    )
-
-
-def export_results(
-    work_dir: Path,
-    output_dir: Path,
-    sample_name: str,
-    requested_artifacts: list[PipelineArtifact],
-    result_file_mapping: dict[PipelineArtifact, list[str]],
-) -> None:
-    for artifact in requested_artifacts:
-        if artifact == PipelineArtifact.DEBUG:
-            logger.info(f"Skipping export of {artifact}")
-            continue
-        for file in result_file_mapping[artifact]:
-            (output_dir / sample_name / file).parent.mkdir(exist_ok=True, parents=True)
-            shutil.copy(work_dir / sample_name / file, output_dir / sample_name / file)
-
-
-if __name__ == "__main__":
-    main()