diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf
index ba347fb16c1..bff3654cd95 100644
--- a/modules/nf-core/bcftools/query/main.nf
+++ b/modules/nf-core/bcftools/query/main.nf
@@ -34,7 +34,7 @@ process BCFTOOLS_QUERY {
         $samples_file \\
         $args \\
         $vcf \\
-        > ${prefix}.txt
+        > ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":