diff --git a/modules/nf-core/miniasm/main.nf b/modules/nf-core/miniasm/main.nf
index afb4c0e327bc..25296e91908d 100644
--- a/modules/nf-core/miniasm/main.nf
+++ b/modules/nf-core/miniasm/main.nf
@@ -13,7 +13,7 @@ process MINIASM {
     output:
     tuple val(meta), path("*.gfa.gz")  , emit: gfa
     tuple val(meta), path("*.fasta.gz"), emit: assembly
-    path "versions.yml"                , emit: versions
+    tuple val("${task.process}"), val('miniasm'), eval('miniasm -V 2>&1'), emit: versions_miniasm, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,10 +33,6 @@ process MINIASM {
     gzip -n ${prefix}.gfa
     gzip -n ${prefix}.fasta
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        miniasm: \$( miniasm -V 2>&1 )
-    END_VERSIONS
     """
 
     stub:
@@ -45,10 +41,6 @@ process MINIASM {
     echo "" | gzip > ${prefix}.gfa.gz
     echo "" | gzip > ${prefix}.fasta.gz
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        miniasm: \$( miniasm -V 2>&1 )
-    END_VERSIONS
     """
 
 }
diff --git a/modules/nf-core/miniasm/meta.yml b/modules/nf-core/miniasm/meta.yml
index 52fea6d77b96..54293b55b640 100644
--- a/modules/nf-core/miniasm/meta.yml
+++ b/modules/nf-core/miniasm/meta.yml
@@ -56,13 +56,27 @@ output:
           pattern: "*.fasta.gz"
           ontologies:
             - edam: http://edamontology.org/format_3989 # GZIP format
+  versions_miniasm:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - miniasm:
+          type: string
+          description: The tool name
+      - miniasm -V 2>&1:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - miniasm:
+          type: string
+          description: The name of the tool
+      - miniasm -V 2>&1:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@avantonder"
 maintainers:
diff --git a/modules/nf-core/miniasm/tests/main.nf.test.snap b/modules/nf-core/miniasm/tests/main.nf.test.snap
index 005c425ddaa5..fb066c692da1 100644
--- a/modules/nf-core/miniasm/tests/main.nf.test.snap
+++ b/modules/nf-core/miniasm/tests/main.nf.test.snap
@@ -21,7 +21,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,0572fb9059c7518d698bc5d609d63935"
+                    [
+                        "MINIASM",
+                        "miniasm",
+                        "0.3-r179"
+                    ]
                 ],
                 "assembly": [
                     [
@@ -41,16 +45,20 @@
                         "test.gfa.gz:md5,60e8b0c635905d20bc5296710749abde"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,0572fb9059c7518d698bc5d609d63935"
+                "versions_miniasm": [
+                    [
+                        "MINIASM",
+                        "miniasm",
+                        "0.3-r179"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2024-05-13T11:09:05.048611538"
+        "timestamp": "2026-01-22T16:50:51.951168082"
     },
     "bacteroides_fragilis - [fastq.gz, paf]- fasta - stub": {
         "content": [
@@ -74,7 +82,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,0572fb9059c7518d698bc5d609d63935"
+                    [
+                        "MINIASM",
+                        "miniasm",
+                        "0.3-r179"
+                    ]
                 ],
                 "assembly": [
                     [
@@ -94,15 +106,19 @@
                         "test.gfa.gz:md5,60e8b0c635905d20bc5296710749abde"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,0572fb9059c7518d698bc5d609d63935"
+                "versions_miniasm": [
+                    [
+                        "MINIASM",
+                        "miniasm",
+                        "0.3-r179"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2024-05-13T11:09:16.769292018"
+        "timestamp": "2026-01-22T16:50:58.724404158"
     }
 }
\ No newline at end of file