From 25fa6ed26d11291b00020546a438206568b8fec0 Mon Sep 17 00:00:00 2001
From: "Pavel V. Dimens" <19176506+pdimens@users.noreply.github.com>
Date: Thu, 30 Jan 2025 09:58:05 -0500
Subject: [PATCH] add precision to zgrep sample demuxing (#189)

adds the `BX:Z:` prefix to the zgrep command to make sure it's only targeting the BX tag in the read header
---
 harpy/snakefiles/demultiplex_gen1.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/harpy/snakefiles/demultiplex_gen1.smk b/harpy/snakefiles/demultiplex_gen1.smk
index 67f1e687..0d38da91 100644
--- a/harpy/snakefiles/demultiplex_gen1.smk
+++ b/harpy/snakefiles/demultiplex_gen1.smk
@@ -98,7 +98,7 @@ rule demultiplex_samples:
         None
     shell:
         """
-        ( zgrep -A3 "A..{params}B..D" {input} | grep -v "^--$" | gzip -q > {output} ) || touch {output}
+        ( zgrep -A3 "BX:Z:A..{params}B..D" {input} | grep -v "^--$" | gzip -q > {output} ) || touch {output}
         """
 
 rule assess_quality: