diff --git a/tools/checkm2/checkm2.xml b/tools/checkm2/checkm2.xml
index b9645388a10..78cc98fc916 100644
--- a/tools/checkm2/checkm2.xml
+++ b/tools/checkm2/checkm2.xml
@@ -17,7 +17,7 @@
     mkdir input_dir &&
     #for $i, $file in enumerate($input):
         #set $cleaned =  re.sub('[^\s\w\-\\.]', '_', str($file.element_identifier))
-        ln -s $file input_dir/${cleaned}.dat &&
+        ln -s '$file' 'input_dir/${cleaned}.dat' &&
     #end for
     checkm2 predict
     --input input_dir