helper script to run the workflow

src/depiction_cluster_sandbox/run_cluster_sandbox.py

@@ -1,5 +1,21 @@
+from pathlib import Path
+
+from depiction_targeted_preproc.workflow.snakemake_invoke import SnakemakeInvoke
+
+work_dir = Path(__file__).parent / "data-sandbox"
+
+
+def available_samples() -> list[str]:
+    return [p.name for p in (work_dir / "raw").glob("*")]
+
+
 def main():
-    pass
+    samples = available_samples()
+    snakefile_path = Path(__file__).parent / "workflow" / "Snakefile"
+    snakemake = SnakemakeInvoke(continue_on_error=False, snakefile_name=snakefile_path)
+    snakemake.invoke(
+        work_dir=work_dir, result_files=[work_dir / sample / "cluster_kmeans_default.hdf5" for sample in samples]
+    )
 
 
 if __name__ == "__main__":