From 3424fdd3046cfc2d34dca38d7250c1d73954f57c Mon Sep 17 00:00:00 2001 From: "Jason M. Wood" Date: Fri, 27 Feb 2026 10:19:58 -0600 Subject: [PATCH] Quote variables that may contain spaces in call to macs2 --- src/pycisTopic/pseudobulk_peak_calling.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/pycisTopic/pseudobulk_peak_calling.py b/src/pycisTopic/pseudobulk_peak_calling.py index 5b66035..c4cabd1 100644 --- a/src/pycisTopic/pseudobulk_peak_calling.py +++ b/src/pycisTopic/pseudobulk_peak_calling.py @@ -536,13 +536,13 @@ def call_peak(self): if self.nolambda is True: cmd = ( self.macs_path - + " callpeak --treatment %s --name %s --outdir %s --format %s --gsize %s " + + " callpeak --treatment \"%s\" --name \"%s\" --outdir \"%s\" --format %s --gsize %s " "--qvalue %s --nomodel --shift %s --extsize %s --keep-dup %s --call-summits --nolambda" ) else: cmd = ( self.macs_path - + " callpeak --treatment %s --name %s --outdir %s --format %s --gsize %s " + + " callpeak --treatment \"%s\" --name \"%s\" --outdir \"%s\" --format %s --gsize %s " "--qvalue %s --nomodel --shift %s --extsize %s --keep-dup %s --call-summits" )