diff --git a/src/depiction_targeted_preproc/example/run.py b/src/depiction_targeted_preproc/example/run.py index 672170b..90214d5 100644 --- a/src/depiction_targeted_preproc/example/run.py +++ b/src/depiction_targeted_preproc/example/run.py @@ -24,9 +24,12 @@ PipelineArtifact.DEBUG: [ "qc/plot_marker_presence_cv.pdf", "qc/plot_spectra_for_marker.pdf", - #"qc/plot_sample_spectra_before_after.pdf", + # "qc/plot_sample_spectra_before_after.pdf", "qc/plot_peak_counts.pdf", - ], + "cluster_default_kmeans.hdf5", + "cluster_default_stats_kmeans.csv", + "cluster_default_kmeans.png" + ] } @@ -39,6 +42,7 @@ def main() -> None: # 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_mcc" # sample_name = "menzha_20231208_s607923_tonsil-repro-sample-01_peptnoise" params_file = Path(__file__).parents[1] / "pipeline_config" / "default.yml" @@ -102,7 +106,7 @@ def initial_setup(input_imzml: Path, input_mass_list: Path, params_file: Path, w def snakemake_invoke(work_dir: Path, result_files: list[Path]) -> None: - snakefile_path = Path(__file__).parents[1] / "workflow" / "Snakefile" + snakefile_path = Path(__file__).parents[1] / "workflow" / "experimental.smk" workflow_dir = Path(__file__).parents[1] / "workflow" snakemake_bin = shutil.which("snakemake")