From 5c886fa439399c129fcec536b6d149b4e1741685 Mon Sep 17 00:00:00 2001
From: Alexander Thomas <77535027+alethomas@users.noreply.github.com>
Date: Thu, 24 Mar 2022 18:55:25 +0100
Subject: [PATCH] fix: primer clipping add up- and downstream (#515)

---
 workflow/rules/read_clipping.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/rules/read_clipping.smk b/workflow/rules/read_clipping.smk
index f2b970cfa..8abdde7ed 100644
--- a/workflow/rules/read_clipping.smk
+++ b/workflow/rules/read_clipping.smk
@@ -57,7 +57,7 @@ rule bamclipper:
         "(cp {input.bam} {params.output_dir} &&"
         " cp {input.bai} {params.output_dir} &&"
         " cd {params.output_dir} &&"
-        " bamclipper.sh -b {params.bam} -p {params.bed_path} -n {threads}) "
+        " bamclipper.sh -b {params.bam} -p {params.bed_path} -n {threads} -u 5 -d 5) "
         " > {params.cwd}/{log} 2>&1"