diff --git a/mergecounts.wdl b/mergecounts.wdl
index c2373f7f02596607f1c9999ecfb35ff49aa6c43a..e93068e325fc7e9fa5e3c0147bea1a6a2a04fe95 100644
--- a/mergecounts.wdl
+++ b/mergecounts.wdl
@@ -9,6 +9,7 @@ task MergeCounts {
     # Based on a script by Szymon Kielbasa/Ioannis Moustakas
     command <<<
         set -e -o pipefail
+        mkdir -p ${sub(outputFile, basename(outputFile) + "$", "")}
         ${preCommand}
         R --no-save --slave <<CODE > ${outputFile}
             library(dplyr)