diff --git a/src/nf_modules/agat/main.nf b/src/nf_modules/agat/main.nf
index 03b1a3f58d7b1f7d10d63feb2ef571d84ee9842a..a2e3d42091138af1844200cddac081a49325fe44 100644
--- a/src/nf_modules/agat/main.nf
+++ b/src/nf_modules/agat/main.nf
@@ -18,6 +18,6 @@ process gff_to_bed {
 
   script:
 """
-agat_convert_sp_gff2bed.pl --gff ${gff} -o ${gff.simpleName}.bed
+agat_convert_sp_gff2bed.pl --gff ${gff} --sub cds -o ${gff.simpleName}.bed
 """
 }
\ No newline at end of file