diff --git a/tools/halfdeep/halfdeep.xml b/tools/halfdeep/halfdeep.xml
index be55c582957..d6da4d790c6 100644
--- a/tools/halfdeep/halfdeep.xml
+++ b/tools/halfdeep/halfdeep.xml
@@ -30,9 +30,9 @@
         ## mapped reads
         ##
         #if $mapped_reads
-            ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}.bam' &&
-            ln -s '${reads_base}.bam' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam' &&
-            ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam.bai' &&
+            ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}${reads.ext}.bam' &&
+            ln -s '${reads_base}${reads.ext}.bam' 'halfdeep/ref/mapped_reads/${reads_base}${reads.ext}.sort.bam' &&
+            ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}{reads.ext}.sort.bam.bai' &&
         #end if
         ##
         ## run bam_depth.sh
diff --git a/tools/halfdeep/macros.xml b/tools/halfdeep/macros.xml
index 25ef5b7322d..536f15b4d8e 100644
--- a/tools/halfdeep/macros.xml
+++ b/tools/halfdeep/macros.xml
@@ -5,7 +5,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">0.1.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="citations">
         <citations>