more plots for the poster

fgcz · Jun 7, 2024 · 037b569 · 037b569
1 parent 18d57f3
commit 037b569
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Showing 3 changed files with 6 additions and 1 deletion.
diff --git a/src/depiction_targeted_preproc/example_compare/run_compare.py b/src/depiction_targeted_preproc/example_compare/run_compare.py
@@ -36,6 +36,9 @@ def main() -> None:
     for imzml in imzmls:
         requested_files += prepare_tasks(data_raw_dir / imzml, work_dir=work_dir)
 
+    ## TODO quick hack
+    #requested_files = [f for f in requested_files if "mini" in str(f)]
+
     SnakemakeInvoke(continue_on_error=True).invoke(work_dir=work_dir, result_files=requested_files, n_cores=4)
 
 

diff --git a/src/depiction_targeted_preproc/workflow/exp/mass_list_preparation.py b/src/depiction_targeted_preproc/workflow/exp/mass_list_preparation.py
@@ -33,7 +33,7 @@ def exp_mass_list_preparation(
     visualization_df.write_csv(out_visualization_csv_path)
 
     if out_visualization_mini_csv_path:
-        choices = ["Angiotensin standard", "CD38", "CD20", "Caveolin-1", "VIM", "CD36", "FN1", "Ki67"]
+        choices = ["Angiotensin standard", "CD38", "CD20", "Caveolin-1", "VIM", "CD36", "FN1", "Ki67", "CD16", "GATA3"]
         visualization_mini_df = visualization_df.filter(pl.col("label").is_in(choices))
         visualization_mini_df.write_csv(out_visualization_mini_csv_path)
 

diff --git a/src/depiction_targeted_preproc/workflow/snakemake_invoke.py b/src/depiction_targeted_preproc/workflow/snakemake_invoke.py
@@ -66,6 +66,8 @@ def _invoke_subprocess(self, work_dir: Path, result_files: list[Path], n_cores:
             str(n_cores),
             "--snakefile",
             str(self.snakefile_path),
+            # TODO configurable
+            "--rerun-incomplete",
             *extra_args,
             *[str(file.relative_to(work_dir)) for file in result_files],
         ]