some small fixes

src/depiction_targeted_preproc/example_compare/run_compare.py

@@ -34,7 +34,7 @@ def main() -> None:
     for imzml in imzmls:
         requested_files += prepare_tasks(data_raw_dir / imzml, work_dir=work_dir)
 
-    SnakemakeInvoke().invoke(work_dir=work_dir, result_files=requested_files, n_cores=2)
+    SnakemakeInvoke().invoke(work_dir=work_dir, result_files=requested_files, n_cores=4)
 
 
 def get_all_output_files(folders: list[Path]) -> list[Path]:

src/depiction_targeted_preproc/workflow/exp/mass_list_preparation.py

@@ -21,10 +21,10 @@ def exp_mass_list_preparation(
     visualization_df = input_df.with_columns(tol=pl.lit(0.25))
 
     # for the calibration remove the CHCA peaks, they have names starting with CHCA
-    calibration_df = visualization_df.filter(~pl.col("name").str.starts_with("CHCA"))
+    calibration_df = visualization_df.filter(~pl.col("label").str.starts_with("CHCA"))
 
     # for the standards csv only keep the "standard" peaks
-    standards_df = visualization_df.filter(pl.col("name").str.to_lowercase().contains("standard"))
+    standards_df = visualization_df.filter(pl.col("label").str.to_lowercase().str.contains("standard"))
 
     # write the results
     calibration_df.write_csv(out_calibration_csv_path)

src/depiction_targeted_preproc/workflow/experimental.smk

@@ -23,10 +23,10 @@ rule exp_mass_list_preparation:
     output:
         calibration_csv="{sample}/mass_list.calibration.csv",
         standards_csv="{sample}/mass_list.standards.csv",
-        visualization="{sample}/mass_list.visualization.csv"
+        visualization_csv="{sample}/mass_list.visualization.csv"
     shell:
         "python -m depiction_targeted_preproc.workflow.exp.mass_list_preparation"
         " --input-csv-path {input.csv}"
-        " --out-calibration-csv {output.calibration_csv}"
-        " --out-standards-csv {output.standards_csv}"
-        " --out-visualization {output.visualization}"
+        " --out-calibration-csv-path {output.calibration_csv}"
+        " --out-standards-csv-path {output.standards_csv}"
+        " --out-visualization-csv-path {output.visualization_csv}"