diff --git a/tools/bioext/bam2msa.xml b/tools/bioext/bam2msa.xml
index 2f082956a87..f8882139698 100644
--- a/tools/bioext/bam2msa.xml
+++ b/tools/bioext/bam2msa.xml
@@ -7,11 +7,14 @@
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
+        ## avoid bam2msa to create .bai in inputdir
+        ln -s '$input' input_bam &&
+        ln -s '$input.metadata.bam_index' input_bam.bai &&
         bam2msa
             #if $region_start and $region_end:
                 -r $region_start:$region_end
             #end if
-            '$input' '$output'
+            'input_bam' '$output'
         ]]></command>
     <inputs>
         <param name="input" type="data" format="bam,sam" label="Input BAM file"/>