diff --git a/conf/test_stub.config b/conf/test_stub.config
index 4b8970de..b0a99ed0 100644
--- a/conf/test_stub.config
+++ b/conf/test_stub.config
@@ -29,11 +29,8 @@ params {
             fasta           = "temp/GRCh38.fasta"
             fai             = "temp/GRCh38.fai"
             dict            = "temp/GRCh38.dict"
-            bwa_index       = "temp/GRCh38_bwa/"
-            bwa_index_image = "temp/GRCh38.img"
-            bwa_index_bseq  = "temp/GRCh38.fasta.0123"
-            bwa_index_biidx = "temp/GRCh38.fasta.bwt.2bit.64"
-            gridss_index    = "temp/GRCh38.gridsscache"
+            bwa_index       = "temp/GRCh38_bwa-mem2_index/"
+            gridss_index    = "temp/GRCh38_gridss_index/"
             star_index      = "temp/GRCh38_star_index/"
         }