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Move checking age of runfolder earlier to fix bug #553

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merged 1 commit into from
Jul 11, 2024
Merged

Move checking age of runfolder earlier to fix bug #553

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24 changes: 12 additions & 12 deletions wscleaner/wscleaner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -147,11 +147,11 @@ def get_runfolders_to_process(self) -> list:
)
rf_obj = RunfolderObject(folder_name, RunfolderCleanupConfig.TIMESTAMP)
rf_age = rf_obj.age()
if os.path.exists(os.path.join(self.samplesheets_dir, f"{folder_name}_SampleSheet.csv")):
rf_samples_obj = RunfolderSamples(rf_obj, script_logger)
if rf_samples_obj:
if os.path.exists(rf_obj.rtacompletefile_path):
if (rf_age >= self.min_age):
if (rf_age >= self.min_age):
if os.path.exists(os.path.join(self.samplesheets_dir, f"{folder_name}_SampleSheet.csv")):
rf_samples_obj = RunfolderSamples(rf_obj, script_logger)
if rf_samples_obj:
if os.path.exists(rf_obj.rtacompletefile_path):
# Catch TSO500 runfolders here (do not contain fastqs)
if rf_samples_obj.pipeline == "dev":
script_logger.info(
Expand Down Expand Up @@ -183,16 +183,16 @@ def get_runfolders_to_process(self) -> list:
)
else:
script_logger.info(
f"{rf_obj.runfolder_name} is < {self.min_age} days old"
f"{rf_obj.runfolder_name} is not a runfolder, or sequencing has not yet finished"
)
else:
script_logger.info(
f"{rf_obj.runfolder_name} is not a runfolder, or sequencing has not yet finished"
)
else:
script_logger.info(
f"Corresponding SampleSheet for {rf_obj.runfolder_name} could not be located. This is required for analysing for deletion"
)
else:
script_logger.info(
f"Corresponding SampleSheet for {rf_obj.runfolder_name} could not be located. This is required for analysing for deletion"
)
f"{rf_obj.runfolder_name} is < {self.min_age} days old"
)
to_assess = [rf_obj.runfolder_name for runfolder_object in runfolder_objects]
all_folders = [folder.split("/")[-1].strip() for folder in folders]
to_skip = [folder for folder in all_folders if folder not in to_assess]
Expand Down
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