diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf
index 0a775ebebb2..bff3654cd95 100644
--- a/modules/nf-core/bcftools/query/main.nf
+++ b/modules/nf-core/bcftools/query/main.nf
@@ -14,8 +14,8 @@ process BCFTOOLS_QUERY {
     path samples
 
     output:
-    tuple val(meta), path("*.txt"), emit: txt
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.${suffix}"), emit: output
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,6 +23,7 @@ process BCFTOOLS_QUERY {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    suffix = task.ext.suffix ?: "txt"
     def regions_file = regions ? "--regions-file ${regions}" : ""
     def targets_file = targets ? "--targets-file ${targets}" : ""
     def samples_file =  samples ? "--samples-file ${samples}" : ""
@@ -33,7 +34,7 @@ process BCFTOOLS_QUERY {
         $samples_file \\
         $args \\
         $vcf \\
-        > ${prefix}.txt
+        > ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -43,8 +44,9 @@ process BCFTOOLS_QUERY {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    suffix = task.ext.suffix ?: "txt"
     """
-    touch ${prefix}.txt \\
+    touch ${prefix}.${suffix} \\
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/bcftools/query/meta.yml b/modules/nf-core/bcftools/query/meta.yml
index fd4fd473910..67302ceda69 100644
--- a/modules/nf-core/bcftools/query/meta.yml
+++ b/modules/nf-core/bcftools/query/meta.yml
@@ -48,10 +48,9 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - txt:
+  - output:
       type: file
       description: BCFTools query output file
-      pattern: "*.txt"
   - versions:
       type: file
       description: File containing software versions
diff --git a/tests/modules/nf-core/bcftools/query/test.yml b/tests/modules/nf-core/bcftools/query/test.yml
index 7acf1880dbd..c2b8701d3b8 100644
--- a/tests/modules/nf-core/bcftools/query/test.yml
+++ b/tests/modules/nf-core/bcftools/query/test.yml
@@ -1,8 +1,8 @@
 - name: bcftools query test_bcftools_query
   command: nextflow run ./tests/modules/nf-core/bcftools/query -entry test_bcftools_query -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/query/nextflow.config
   tags:
-    - bcftools
     - bcftools/query
+    - bcftools
   files:
     - path: output/bcftools/out.txt
       md5sum: 51d135de052f3bcef50dcd6b74806094
@@ -11,8 +11,8 @@
 - name: bcftools query test_bcftools_query_with_optional_files
   command: nextflow run ./tests/modules/nf-core/bcftools/query -entry test_bcftools_query_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/query/nextflow.config
   tags:
-    - bcftools
     - bcftools/query
+    - bcftools
   files:
     - path: output/bcftools/out.txt
       md5sum: 1785d1957ba7206df852d0689b91753f