From 005a9d6e7d947dabcd15e67c5f20f9acce3fa019 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 23 Jan 2020 10:46:40 +0100
Subject: [PATCH] set pipefail to prevent errors in bed files
---
bedtools.wdl | 1 +
1 file changed, 1 insertion(+)
diff --git a/bedtools.wdl b/bedtools.wdl
index 407250f..50f9f92 100644
--- a/bedtools.wdl
+++ b/bedtools.wdl
@@ -102,6 +102,7 @@ task MergeBedFiles {
# A sorted bed is needed for bedtools merge
command {
+ set -e -o pipefail
cat ~{sep=" " bedFiles} | bedtools sort | bedtools merge > ~{outputBed}
}
--
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