diff --git a/bwa.wdl b/bwa.wdl
index 2845c32e877bb3c617964e47ea62a2c90a347523..90b017fc26583fe88d54ce5d4099c4cd85d1901f 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -52,8 +52,7 @@ task index {
     }
 
     output {
-        File indexBase = if (defined(outputDir)) then select_first([outputDir]) + "/" + fastaFilename else fastaFilename
-        File indexedFasta = indexBase
+        File indexedFasta = outputFile
         Array[File] indexFiles = [indexBase + ".bwt",indexBase + ".pac",indexBase + ".sa",indexBase + ".amb",indexBase + ".ann"]
     }
     parameter_meta {