diff --git a/bwa.wdl b/bwa.wdl
index 5839a9c0c968891cdc523a361deee796fcebe30f..ffa42313dad13f0c13df6f9c77f938567c0027a0 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -40,7 +40,10 @@ task index {
         set -e -o pipefail
         ${"mkdir -p " + outputDir}
         ${preCommand}
-        ln -sf ${fasta} ${outputDir + "/"}${fastaFilename}
+        if [[ ! '${outputDir}' =  '' ]]
+        then
+            ln -sf ${fasta} ${outputDir + "/"}${fastaFilename}
+        fi
         bwa index \
         ${"-a " + constructionAlgorithm} \
         ${"-b" + blockSize} \