diff --git a/bedtools.wdl b/bedtools.wdl
index 407250fe97127ddb23e643223335a5e0fc22bfff..50f9f92e1b49afc5e393084270d5768a06117fb8 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}
     }