diff --git a/tools/tetyper/tetyper.xml b/tools/tetyper/tetyper.xml
index cb1a65cbd78..cdbb6c42fea 100644
--- a/tools/tetyper/tetyper.xml
+++ b/tools/tetyper/tetyper.xml
@@ -8,6 +8,8 @@
     </requirements>
     <command detect_errors="exit_code">
         <![CDATA[
+        ## avoid creating indices in the inputdir
+        ln -s '$reference' reference.fa &&
         TETyper.py
             --threads \${GALAXY_SLOTS:-1}
             #if $collection_paired.selector == "paired"
@@ -15,7 +17,7 @@
             #elif $collection_paired.selector == "collection":
                 --fq1 '${collection_paired.input_pair.forward}' --fq2 '${collection_paired.input_pair.reverse}'
             #end if
-            --ref '${reference}'
+            --ref 'reference.fa'
             --flank_len '${flank_length}'
             --min_reads '${min_reads}'
             --min_each_strand '${min_each_strand}'