diff --git a/modules/nf-core/fq/generate/main.nf b/modules/nf-core/fq/generate/main.nf
index 95a06a1b6ff3..155fd0b4ea17 100644
--- a/modules/nf-core/fq/generate/main.nf
+++ b/modules/nf-core/fq/generate/main.nf
@@ -11,8 +11,8 @@ process FQ_GENERATE {
     val meta
 
     output:
-    tuple val(meta), path("*.fastq.gz"), emit: fastq
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path("*.fastq.gz")                                                                      , emit: fastq
+    tuple val("${task.process}"), val('fq'), eval("fq generate --version | sed 's/fq-generate //;s/ (.*//' "), emit: versions_fq, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,22 +24,12 @@ process FQ_GENERATE {
     fq generate \\
         $args \\
         ${prefix}_R1.fastq.gz ${prefix}_R2.fastq.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fq: \$(echo \$(fq generate --version | sed 's/fq-generate //g'))
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    echo | gzip > ${prefix}_R1.fastq.gz
-    echo | gzip > ${prefix}_R2.fastq.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fq: \$(echo \$(fq generate --version | sed 's/fq-generate //g'))
-    END_VERSIONS
+    echo "" | gzip > ${prefix}_R1.fastq.gz
+    echo "" | gzip > ${prefix}_R2.fastq.gz
     """
 }
diff --git a/modules/nf-core/fq/generate/meta.yml b/modules/nf-core/fq/generate/meta.yml
index 0563da01e42c..8b8795d69bd3 100644
--- a/modules/nf-core/fq/generate/meta.yml
+++ b/modules/nf-core/fq/generate/meta.yml
@@ -12,7 +12,8 @@ tools:
       homepage: "https://github.com/stjude-rust-labs/fq"
       documentation: "https://github.com/stjude-rust-labs/fq"
       tool_dev_url: "https://github.com/stjude-rust-labs/fq"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - meta:
@@ -32,14 +33,28 @@ output:
           description: Random generated FASTQ files.
           pattern: "*_R[12].fastq.gz"
           ontologies:
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: http://edamontology.org/format_3989
+  versions_fq:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - fq:
+          type: string
+          description: The name of the tool
+      - "fq generate --version | sed 's/fq-generate //;s/ (.*//' ":
+          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
+      - fq:
+          type: string
+          description: The name of the tool
+      - "fq generate --version | sed 's/fq-generate //;s/ (.*//' ":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@adamrtalbot"
 maintainers:
diff --git a/modules/nf-core/fq/generate/tests/main.nf.test.snap b/modules/nf-core/fq/generate/tests/main.nf.test.snap
index 25b8a481b5e6..978989fa2326 100644
--- a/modules/nf-core/fq/generate/tests/main.nf.test.snap
+++ b/modules/nf-core/fq/generate/tests/main.nf.test.snap
@@ -15,7 +15,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,cacd942133fef4aada49329843f0a582"
+                    [
+                        "FQ_GENERATE",
+                        "fq",
+                        "0.12.0"
+                    ]
                 ],
                 "fastq": [
                     [
@@ -29,16 +33,20 @@
                         ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,cacd942133fef4aada49329843f0a582"
+                "versions_fq": [
+                    [
+                        "FQ_GENERATE",
+                        "fq",
+                        "0.12.0"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-05-01T12:15:33.190349",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-10-19T16:38:52.818166434"
+            "nf-test": "0.9.4",
+            "nextflow": "26.04.0"
+        }
     },
     "test fq": {
         "content": [
@@ -56,7 +64,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,cacd942133fef4aada49329843f0a582"
+                    [
+                        "FQ_GENERATE",
+                        "fq",
+                        "0.12.0"
+                    ]
                 ],
                 "fastq": [
                     [
@@ -70,15 +82,19 @@
                         ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,cacd942133fef4aada49329843f0a582"
+                "versions_fq": [
+                    [
+                        "FQ_GENERATE",
+                        "fq",
+                        "0.12.0"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-05-01T12:15:29.873962",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-10-19T16:38:39.365406108"
+            "nf-test": "0.9.4",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file