diff --git a/modules/local/svprep/assemble/main.nf b/modules/local/svprep/assemble/main.nf
index 08bdb91e..0ef0cf36 100644
--- a/modules/local/svprep/assemble/main.nf
+++ b/modules/local/svprep/assemble/main.nf
@@ -69,7 +69,7 @@ process GRIDSS_ASSEMBLE {
     done
 
     # Symlink indices next to assembly FASTA
-    ln -s \$(find -L ${genome_gridss_index} -type f) ./
+    ln -s \$(find -L ${genome_gridss_index} -regex '.*\.\(amb\|ann\|pac\|gridsscache\|sa\|bwa\|img\|alt\)') ./
 
     # Run
     gridss_svprep \\
diff --git a/modules/local/svprep/call/main.nf b/modules/local/svprep/call/main.nf
index 3cbb62c4..fd0121d8 100644
--- a/modules/local/svprep/call/main.nf
+++ b/modules/local/svprep/call/main.nf
@@ -67,7 +67,7 @@ process GRIDSS_CALL {
     shadow_input_directory ${assemble_dir}
 
     # Symlink indices next to assembly FASTA
-    ln -s \$(find -L ${genome_gridss_index} -type f) ./
+    ln -s \$(find -L ${genome_gridss_index} -regex '.*\.\(amb\|ann\|pac\|gridsscache\|sa\|bwa\|img\|alt\)') ./
 
     # Run
     gridss_svprep \\
diff --git a/modules/local/svprep/preprocess/main.nf b/modules/local/svprep/preprocess/main.nf
index ed3f3430..cd9ee75c 100644
--- a/modules/local/svprep/preprocess/main.nf
+++ b/modules/local/svprep/preprocess/main.nf
@@ -29,7 +29,7 @@ process GRIDSS_PREPROCESS {
 
     """
     # Symlink indices next to assembly FASTA
-    ln -s \$(find -L ${genome_gridss_index} -type f) ./
+    ln -s \$(find -L ${genome_gridss_index} -regex '.*\.\(amb\|ann\|pac\|gridsscache\|sa\|bwa\|img\|alt\)') ./
 
     gridss_svprep \\
         ${args} \\
diff --git a/modules/local/virusbreakend/main.nf b/modules/local/virusbreakend/main.nf
index 6ec6438a..ac23d2f2 100644
--- a/modules/local/virusbreakend/main.nf
+++ b/modules/local/virusbreakend/main.nf
@@ -29,7 +29,7 @@ process VIRUSBREAKEND {
 
     """
     # Symlink indices next to assembly FASTA
-    ln -s \$(find -L ${genome_gridss_index} -type f -name *.gridsscache -o -name *.img) ./
+    ln -s \$(find -L ${genome_gridss_index} -regex '.*\.\(amb\|ann\|pac\|gridsscache\|sa\|bwa\|img\|alt\)') ./
 
     virusbreakend \\
         ${args} \\