diff --git a/biopet.wdl b/biopet.wdl
index a3ecdd01282fc8579cf9a5db6e514b29f6f99bc8..335f26d58cb721fc379b7b143ffeb2d28ffe80f5 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -97,6 +97,8 @@ task ExtractAdaptersFastqc {
         set -e
         ~{preCommand}
         mkdir -p ~{outputDir}
+        touch ~{adapterOutputFilePath}
+        touch ~{contamsOutputFilePath}
         ~{toolCommand} \
         --inputFile ~{inputFile} \
         ~{"--adapterOutputFile " + adapterOutputFilePath } \