diff --git a/tests/software/bwa/test.yml b/tests/software/bwa/test.yml
index 9efefa1d..b92025ec 100644
--- a/tests/software/bwa/test.yml
+++ b/tests/software/bwa/test.yml
@@ -4,13 +4,13 @@
     - bwa
     - bwa_index
   files:
-    - path: output/bwa/NC_010473.fa.amb
+    - path: output/bwa/bwa/NC_010473.fa.amb
       md5sum: 942a990ae872f1c0b8d72dda2db405d5
-    - path: output/bwa/NC_010473.fa.bwt
+    - path: output/bwa/bwa/NC_010473.fa.bwt
       md5sum: 7301b52e2ecb893d429a49fa692447ae
-    - path: output/bwa/NC_010473.fa.pac
+    - path: output/bwa/bwa/NC_010473.fa.pac
       md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
-    - path: output/bwa/NC_010473.fa.sa
+    - path: output/bwa/bwa/NC_010473.fa.sa
       md5sum: a47dcc92e750e2f16fbd979b8ff9538e
 
 - name: Run bwa mem single-end