diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf
index 59bf8d12771a..c33eacec9c19 100644
--- a/modules/nf-core/samtools/mpileup/main.nf
+++ b/modules/nf-core/samtools/mpileup/main.nf
@@ -13,7 +13,7 @@ process SAMTOOLS_MPILEUP {
 
     output:
     tuple val(meta), path("*.mpileup.gz"), emit: mpileup
-    path  "versions.yml"                 , emit: versions
+    tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -1 | sed -e "s/samtools //"'), emit: versions_samtools, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,21 +31,11 @@ process SAMTOOLS_MPILEUP {
         $intervals_cmd \\
         $input
     bgzip ${prefix}.mpileup
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo | gzip > ${prefix}.mpileup.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/samtools/mpileup/meta.yml b/modules/nf-core/samtools/mpileup/meta.yml
index e809fec40eb0..4203f2313999 100644
--- a/modules/nf-core/samtools/mpileup/meta.yml
+++ b/modules/nf-core/samtools/mpileup/meta.yml
@@ -54,16 +54,31 @@ output:
           description: mpileup file
           pattern: "*.{mpileup}"
           ontologies: []
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - samtools:
+          type: string
+          description: Name of the tool
+      - samtools --version | head -1 | sed -e "s/samtools //":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - samtools:
+          type: string
+          description: Name of the tool
+      - samtools --version | head -1 | sed -e "s/samtools //":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@drpatelh"
   - "@joseespinosa"
 maintainers:
-  - "@drpatelh"
   - "@joseespinosa"
diff --git a/modules/nf-core/samtools/mpileup/tests/main.nf.test b/modules/nf-core/samtools/mpileup/tests/main.nf.test
index c4b9f6dfe7f8..1650df7a2d93 100644
--- a/modules/nf-core/samtools/mpileup/tests/main.nf.test
+++ b/modules/nf-core/samtools/mpileup/tests/main.nf.test
@@ -27,10 +27,7 @@ nextflow_process {
         then {
             assert process.success
             assertAll(
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                    ).match() }
+                { assert snapshot(process.out).match()}
             )
         }
     }
@@ -56,10 +53,7 @@ nextflow_process {
         then {
             assert process.success
             assertAll(
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                    ).match() }
+                { assert snapshot(process.out).match()}
             )
         }
     }
@@ -82,10 +76,7 @@ nextflow_process {
         then {
             assert process.success
             assertAll(
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                    ).match() }
+                { assert snapshot(process.out).match()}
             )
         }
     }
diff --git a/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap b/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap
index 4d08c2f9cc47..0d44126e4d86 100644
--- a/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap
@@ -11,7 +11,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e5a70b6d7e2c2ff0c2c63b66b7adb281"
+                    [
+                        "SAMTOOLS_MPILEUP",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ],
                 "mpileup": [
                     [
@@ -21,21 +25,20 @@
                         "test.mpileup.gz:md5,72340047c1feda82fa632d1762080bd8"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e5a70b6d7e2c2ff0c2c63b66b7adb281"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_MPILEUP",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
-            },
-            {
-                "SAMTOOLS_MPILEUP": {
-                    "samtools": "1.22.1"
-                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-09-10T14:39:24.687853"
+        "timestamp": "2025-12-22T08:56:18.583305677"
     },
     "bam_bed --stub": {
         "content": [
@@ -49,7 +52,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e5a70b6d7e2c2ff0c2c63b66b7adb281"
+                    [
+                        "SAMTOOLS_MPILEUP",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ],
                 "mpileup": [
                     [
@@ -59,21 +66,20 @@
                         "test.mpileup.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e5a70b6d7e2c2ff0c2c63b66b7adb281"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_MPILEUP",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
-            },
-            {
-                "SAMTOOLS_MPILEUP": {
-                    "samtools": "1.22.1"
-                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-09-10T14:39:35.387828"
+        "timestamp": "2025-12-22T08:54:55.388446375"
     },
     "bam_bed_fasta": {
         "content": [
@@ -87,7 +93,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e5a70b6d7e2c2ff0c2c63b66b7adb281"
+                    [
+                        "SAMTOOLS_MPILEUP",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ],
                 "mpileup": [
                     [
@@ -97,20 +107,19 @@
                         "test.mpileup.gz:md5,958e6bead4103d72026f80153b6b5150"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e5a70b6d7e2c2ff0c2c63b66b7adb281"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_MPILEUP",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
-            },
-            {
-                "SAMTOOLS_MPILEUP": {
-                    "samtools": "1.22.1"
-                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-09-10T14:39:29.744452"
+        "timestamp": "2025-12-22T08:56:25.883836102"
     }
 }
\ No newline at end of file