diff --git a/src/nf_modules/agat/main.nf b/src/nf_modules/agat/main.nf
index a2e3d42091138af1844200cddac081a49325fe44..b12d2b849fe24540caaf83395f20bea46bcf6fac 100644
--- a/src/nf_modules/agat/main.nf
+++ b/src/nf_modules/agat/main.nf
@@ -18,6 +18,7 @@ process gff_to_bed {
 
   script:
 """
-agat_convert_sp_gff2bed.pl --gff ${gff} --sub cds -o ${gff.simpleName}.bed
+zcat ${gff} > ${gff.baseName}.gff
+agat_convert_sp_gff2bed.pl --gff ${gff.baseName}.gff --sub cds -o ${gff.simpleName}.bed
 """
 }
\ No newline at end of file