Fixed flake8

relecov_tools/assets/pipeline_utils/viralrecon.py

@@ -8,7 +8,6 @@
 import os.path
 
 from pathlib import Path
-from datetime import datetime
 
 import relecov_tools.utils
 from relecov_tools.config_json import ConfigJson
@@ -172,7 +171,7 @@ def save_to_file(self, j_list, batch_date):
                 if sample_name in samples_indict:
                     if samples_indict[sample_name] != item:
                         stderr.print(
-                            f"[red]Same sample has different data in both long tables."
+                            f"[red]Same sample {sample_name} has different data in both long tables."
                         )
                         log.error(
                             "Sample %s has different data in %s and new long table. Can't merge."

relecov_tools/read_bioinfo_metadata.py

@@ -871,10 +871,9 @@ def save_splitted_files(self, files_dict, batch_date, output_folder=None):
                         f"Error occurred while parsing '{func_name}': {e}.",
                     )
                     sys.exit(self.log_report.print_log_report(method_name, ["error"]))
-        return
+        return data
 
     def get_multiple_sample_files(self):
-        method_name = f"{self.add_bioinfo_files_path.__name__}:{self.get_multiple_sample_files.__name__}"
         multiple_sample_files = []
         for key in self.software_config.keys():
             if self.software_config[key].get("multiple_samples"):
@@ -906,10 +905,10 @@ def create_bioinfo_file(self):
             batch_dates = str(batch_dates[0])
         else:
             stderr.print(
-                f"[orange]More than one batch date in the same json data. Using current date as batch date."
+                "[orange]More than one batch date in the same json data. Using current date as batch date."
             )
             log.info(
-                "]More than one batch date in the same json data. Using current date as batch date."
+                "More than one batch date in the same json data. Using current date as batch date."
             )
             batch_dates = datetime.now().strftime("%Y%m%d%H%M%S")