From b713d391351ae2cdeedfd737422400cdd3dd65fb Mon Sep 17 00:00:00 2001 From: "Kelly Sovacool, PhD" Date: Wed, 8 Jul 2026 12:35:03 -0400 Subject: [PATCH 1/2] fix(run): regex pattern for sample name extraction --- src/xavier/run.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/xavier/run.py b/src/xavier/run.py index eeb823c..8a8c1fe 100644 --- a/src/xavier/run.py +++ b/src/xavier/run.py @@ -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 From e2a9d2113ed8a50815c7f994e3d3e6628f8bf638 Mon Sep 17 00:00:00 2001 From: "Kelly Sovacool, PhD" Date: Wed, 8 Jul 2026 12:36:09 -0400 Subject: [PATCH 2/2] docs: Update CHANGELOG with syntax warning fix Added a syntax warning fix entry to the changelog. --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6f284b7..6b57060 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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)