diff --git a/cutadapt.wdl b/cutadapt.wdl
index afa1b29227d51f7003249e88d35edb3eb00699cb..4a94961ce580146fb88dda402ec61010903ad7e7 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -57,6 +57,7 @@ task cutadapt {
 
     command {
         set -e -o pipefail
+        mkdir -p $(dirname ${read1output})
         ${preCommand}
         cutadapt \
         ${"--cores=" + cores} \