diff --git a/tools/falco/falco.xml b/tools/falco/falco.xml
index 15d2dc03961..5d5e05a8a36 100644
--- a/tools/falco/falco.xml
+++ b/tools/falco/falco.xml
@@ -22,6 +22,8 @@
             #set format = 'bam'
         #elif 'sam' in $input_file.ext:
             #set format = 'sam'
+        #elif 'gz' in $input_file.ext:
+            #set format = 'fastq.gz'
         #else
             #set format = 'fastq'
         #end if