diff --git a/modules/samtools/mpileup/main.nf b/modules/samtools/mpileup/main.nf
index fcd498be..cfab5c98 100644
--- a/modules/samtools/mpileup/main.nf
+++ b/modules/samtools/mpileup/main.nf
@@ -11,8 +11,8 @@ process SAMTOOLS_MPILEUP {
     path  fasta
 
     output:
-    tuple val(meta), path("*.mpileup"), emit: mpileup
-    path  "versions.yml"              , emit: versions
+    tuple val(meta), path("*.mpileup.gz"), emit: mpileup
+    path  "versions.yml"                           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,6 +27,7 @@ process SAMTOOLS_MPILEUP {
         --output ${prefix}.mpileup \\
         $args \\
         $input
+    bgzip ${prefix}.mpileup
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/tests/modules/samtools/mpileup/test.yml b/tests/modules/samtools/mpileup/test.yml
index c3d794d0..8834f639 100644
--- a/tests/modules/samtools/mpileup/test.yml
+++ b/tests/modules/samtools/mpileup/test.yml
@@ -4,8 +4,8 @@
     - samtools
     - samtools/mpileup
   files:
-    - path: output/samtools/test.mpileup
-      md5sum: 958e6bead4103d72026f80153b6b5150
+    - path: output/samtools/test.mpileup.gz
+      md5sum: 29455c36377196e8bc9cf831cf17b5dc
     - path: output/samtools/versions.yml
 
 - name: samtools mpileup test_samtools_mpileup_intervals
@@ -14,6 +14,6 @@
     - samtools
     - samtools/mpileup
   files:
-    - path: output/samtools/test.mpileup
-      md5sum: 958e6bead4103d72026f80153b6b5150
+    - path: output/samtools/test.mpileup.gz
+      md5sum: 29455c36377196e8bc9cf831cf17b5dc
     - path: output/samtools/versions.yml