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Broaden ONT transfer script's categorization of QC runs #424

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merged 2 commits into from
May 8, 2024
Merged

Broaden ONT transfer script's categorization of QC runs #424

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0f7ab54
init
kedhammar May 7, 2024
b40dc62
ruff fix
kedhammar May 7, 2024
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4 changes: 4 additions & 0 deletions VERSIONLOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,9 @@
# TACA Version Log

## 20240507.1

Broaden ONT transfer script's categorization of QC runs to either experiment dir or sample dir starting with "QC\_".

## 20240422.1

Refine GHA VERSIONLOG.md check to compare to merge-base, not branch-base.
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5 changes: 3 additions & 2 deletions taca/nanopore/instrument_transfer.py
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Expand Up @@ -50,8 +50,9 @@ def main(args):
for run_path in run_paths:
logging.info(f"Handling {run_path}...")

if run_path.split(os.sep)[-2][0:3] == "QC_":
# For QC runs, the sample name should start with "QC_"
experiment_name = run_path.split(os.sep)[-3]
sample_name = run_path.split(os.sep)[-2]
if sample_name[0:3] == "QC_" or experiment_name[0:3] == "QC_":
logging.info("Run categorized as QC.")
rsync_dest = args.dest_dir_qc
else:
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2 changes: 1 addition & 1 deletion taca/utils/misc.py
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Expand Up @@ -162,7 +162,7 @@ def query_yes_no(question, default="yes", force=False):
elif default == "no":
prompt = " [y/N] "
else:
raise ValueError('invalid default answer: "%s"' % default)
raise ValueError(f'invalid default answer: "{default}"')

while True:
sys.stdout.write(question + prompt)
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