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fix(run): regex pattern for sample name extraction #184

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Merged
kelly-sovacool merged 3 commits into from
Jul 10, 2026
Merged

fix(run): regex pattern for sample name extraction #184

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b713d39
fix(run): regex pattern for sample name extraction
kelly-sovacool Jul 8, 2026
e2a9d21
docs: Update CHANGELOG with syntax warning fix
kelly-sovacool Jul 8, 2026
295e5f9
Merge branch 'main' into iss-183
kelly-sovacool Jul 8, 2026
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
## XAVIER development version

- Fixed syntax warning. (#184, @kelly-sovacool)

## XAVIER 3.2.2

- Fixed a bug where tumor-only and unpaired runs could fail during Snakefile parsing (#174, @samarth8392)
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2 changes: 1 addition & 1 deletion src/xavier/run.py
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Expand Up @@ -655,7 +655,7 @@ def get_nends(ifiles):
nends = {} # keep count of R1 and R2 for each sample
for file in ifiles:
# Split sample name on file extension
sample = re.split("\.R[12]\.fastq\.gz", os.path.basename(file))[0]
sample = re.split(r"\.R[12]\.fastq\.gz", os.path.basename(file))[0]
if sample not in nends:
nends[sample] = 0

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