diff --git a/tools/halfdeep/halfdeep.xml b/tools/halfdeep/halfdeep.xml
index db29477d589..12bd24953de 100644
--- a/tools/halfdeep/halfdeep.xml
+++ b/tools/halfdeep/halfdeep.xml
@@ -5,6 +5,10 @@
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
+        ##
+        ## Set up the directory layout expected by bam_depth.sh and halfdeep.sh
+        ## See: https://github.com/makovalab-psu/HalfDeep?tab=readme-ov-file#expected-directory-layout
+        ##
         #import re
         ##
         ## reference