refactor(geo_submission): remove unnecessary conversion of output_fil…

…e_name to pathlib.Path and simplify processed files handling
alsmith151 · Nov 15, 2024 · 96914af · 96914af
1 parent 8afff39
commit 96914af
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Showing 2 changed files with 2 additions and 8 deletions.
diff --git a/seqnado/design.py b/seqnado/design.py
@@ -999,11 +999,6 @@ def processed_data_files(self) -> pd.DataFrame:
             ),
         )
 
-        # Convert the output file name to a pathlib.Path object
-        df = df.assign(
-            output_file_name=lambda df: df["output_file_name"].apply(pathlib.Path),
-        )
-
         return df
 
     @property

diff --git a/seqnado/workflow/rules/geo_submission.smk b/seqnado/workflow/rules/geo_submission.smk
@@ -39,9 +39,8 @@ def get_symlinked_files(wc: Any = None) -> List[str]:
 
 
 
-    processed_files = geo_files.processed_data_files['output_file_name']
-
-    if processed_files.any():
+    if not geo_files.processed_data_files.empty:
+        processed_files = geo_files.processed_data_files['output_file_name'].tolist()
         processed_files = [outdir / fn for fn in processed_files]
     else:
         processed_files = []