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Sample name parsing #12

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Merged
chenv3 merged 7 commits into from
Sep 22, 2025
Merged

Sample name parsing #12

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f201d60
fix: process sample names to cell ranger names on convertsion from in…
rroutsong Sep 15, 2025
fa012f5
fix: generalize split for with lanes and without
rroutsong Sep 15, 2025
8bfda99
fix: remove trace
rroutsong Sep 15, 2025
3792776
fix: remove double bracket
rroutsong Sep 15, 2025
912d675
fix: change regex to couple more to define naming scheme
rroutsong Sep 16, 2025
8248975
fix: continue before adding to config
rroutsong Sep 16, 2025
38f427e
Merge branch 'main' into sample_name_parsing
rroutsong Sep 16, 2025
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10 changes: 5 additions & 5 deletions src/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -506,15 +506,15 @@ def add_sample_metadata(input_files, config, group=None):
for file in input_files:
# Split sample name on file extension
sample = re.split(r"(_S[0-9]+)(_L[0-9]{3})?\.R[12]\.f(ast)?q.gz", os.path.basename(file))[0]
if os.path.basename(file) == sample:
# Sample has a non-standard name, print warning message
err("Warning: Sample '{0}' has a file name that is not compatible with cellranger! Skipping over input file...".format(os.path.basename(file)))
continue
if sample not in added:
# Only add PE sample information once
added.append(sample)
config['samples'].append(sample)
if os.path.basename(file) == sample:
# Sample has a non-standard name,
# print warning message
err("Warning: Sample '{0}' has a file name that is not compatible with cellranger! Skipping over input file...".format(os.path.basename(file)))
continue

return config


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