diff --git a/modules/ensembl/fasta/recombine/main.nf b/modules/ensembl/fasta/recombine/main.nf
index dfcf7b1..9eb7a4c 100644
--- a/modules/ensembl/fasta/recombine/main.nf
+++ b/modules/ensembl/fasta/recombine/main.nf
@@ -13,6 +13,8 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
+nextflow.enable.types = true
+
 process FASTA_RECOMBINE {
 
     tag "${meta.id}"
@@ -22,11 +24,13 @@ process FASTA_RECOMBINE {
     container "docker.io/ensemblorg/ensembl-genomio:v1.7.0"
 
     input:
-        tuple val(meta), path(fasta_manifest), path(agp)
+        record(meta: Map, fasta_manifest: Path, agp: Path?)
 
     output:
-        tuple val(meta), path("${meta.id}.fa"), emit: recombined_fasta
-        tuple val("${task.process}"), val('fasta_recombine'), eval("fasta_recombine --version"), emit: versions_fasta_recombine, topic: versions
+        record(meta: meta, recombined_fasta: file("${meta.id}.fa"))
+
+    topic:
+        tuple(task.process, 'fasta_recombine', eval("fasta_recombine --version 2>/dev/null || echo unknown")) >> 'versions'
 
     when:
         task.ext.when == null || task.ext.when
diff --git a/modules/ensembl/fasta/recombine/meta.yml b/modules/ensembl/fasta/recombine/meta.yml
index 858aabd..d6347c0 100644
--- a/modules/ensembl/fasta/recombine/meta.yml
+++ b/modules/ensembl/fasta/recombine/meta.yml
@@ -46,16 +46,6 @@ output:
           pattern: "*.fa"
           ontologies:
             - edam: http://edamontology.org/format_1929 # FASTA
-  versions_fasta_recombine:
-    - - ${task.process}:
-          type: string
-          description: The name of the process.
-      - fasta_recombine:
-          type: string
-          description: The name of the tool.
-      - "fasta_recombine --version":
-          type: eval
-          description: The expression to obtain the version of the tool
 topics:
   versions:
     - - ${task.process}:
@@ -64,7 +54,7 @@ topics:
       - fasta_recombine:
           type: string
           description: The name of the tool.
-      - "fasta_recombine --version":
+      - "fasta_recombine --version 2>/dev/null || echo unknown":
           type: eval
           description: The expression to obtain the version of the tool
 authors:
diff --git a/modules/ensembl/fasta/recombine/tests/main.nf.test b/modules/ensembl/fasta/recombine/tests/main.nf.test
index 4448cf7..33d6add 100644
--- a/modules/ensembl/fasta/recombine/tests/main.nf.test
+++ b/modules/ensembl/fasta/recombine/tests/main.nf.test
@@ -24,6 +24,7 @@ nextflow_process {
     tag "modules_ensembl"
     tag "fasta"
     tag "fasta/recombine"
+    topics "versions"
 
     test("stub outputs: header mode") {
 
@@ -38,18 +39,18 @@ nextflow_process {
                 def no_file = file("NO_FILE")
                 no_file.text = ""
 
-                input[0] = [
-                    [ id: 'test' ],
-                    manifest,
-                    no_file
-                ]
+                input[0] = record(meta: [ id: 'test' ], fasta_manifest: manifest, agp: no_file)
                 """
             }
         }
 
         then {
             assert process.trace.tasks().size() == 1
-            assert process.out.recombined_fasta.size() == 1
+            assert process.out[0].size() == 1
+            assert file(process.out[0][0].recombined_fasta).name == 'test.fa'
+            assert topics.versions.size() == 1
+            assert topics.versions[0].size() == 3
+            assert topics.versions[0][0] == 'FASTA_RECOMBINE'
             assert process.success
             assert snapshot(process.out).match()
         }
@@ -67,18 +68,18 @@ nextflow_process {
 
                 def agp = file("test.agp")
                 agp.text = ""
-                input[0] = [
-                    [ id: 'test' ],
-                    manifest,
-                    agp
-                ]
+                input[0] = record(meta: [ id: 'test' ], fasta_manifest: manifest, agp: agp)
                 """
             }
         }
 
         then {
             assert process.trace.tasks().size() == 1
-            assert process.out.recombined_fasta.size() == 1
+            assert process.out[0].size() == 1
+            assert file(process.out[0][0].recombined_fasta).name == 'test.fa'
+            assert topics.versions.size() == 1
+            assert topics.versions[0].size() == 3
+            assert topics.versions[0][0] == 'FASTA_RECOMBINE'
             assert process.success
             assert snapshot(process.out).match()
         }
diff --git a/modules/ensembl/fasta/recombine/tests/main.nf.test.snap b/modules/ensembl/fasta/recombine/tests/main.nf.test.snap
index c138427..59a7453 100644
--- a/modules/ensembl/fasta/recombine/tests/main.nf.test.snap
+++ b/modules/ensembl/fasta/recombine/tests/main.nf.test.snap
@@ -3,82 +3,38 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
+                    {
+                        "meta": {
                             "id": "test"
                         },
-                        "test.fa:md5,c40116e7d725da4662e6bdd654f70075"
-                    ]
-                ],
-                "1": [
-                    [
-                        "FASTA_RECOMBINE",
-                        "fasta_recombine",
-                        "1.7.0"
-                    ]
-                ],
-                "recombined_fasta": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fa:md5,c40116e7d725da4662e6bdd654f70075"
-                    ]
-                ],
-                "versions_fasta_recombine": [
-                    [
-                        "FASTA_RECOMBINE",
-                        "fasta_recombine",
-                        "1.7.0"
-                    ]
+                        "recombined_fasta": "test.fa:md5,c40116e7d725da4662e6bdd654f70075"
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-06-11T18:08:46.722339",
+        "timestamp": "2026-09-29T12:53:47.242818",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "stub outputs: header mode": {
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.fa:md5,c40116e7d725da4662e6bdd654f70075"
-                    ]
-                ],
-                "1": [
-                    [
-                        "FASTA_RECOMBINE",
-                        "fasta_recombine",
-                        "1.7.0"
-                    ]
-                ],
-                "recombined_fasta": [
-                    [
-                        {
+                    {
+                        "meta": {
                             "id": "test"
                         },
-                        "test.fa:md5,c40116e7d725da4662e6bdd654f70075"
-                    ]
-                ],
-                "versions_fasta_recombine": [
-                    [
-                        "FASTA_RECOMBINE",
-                        "fasta_recombine",
-                        "1.7.0"
-                    ]
+                        "recombined_fasta": "test.fa:md5,c40116e7d725da4662e6bdd654f70075"
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-06-11T18:08:44.434921",
+        "timestamp": "2026-09-29T12:53:44.690151",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/ensembl/fasta/split/main.nf b/modules/ensembl/fasta/split/main.nf
index ccccffa..c57f67b 100644
--- a/modules/ensembl/fasta/split/main.nf
+++ b/modules/ensembl/fasta/split/main.nf
@@ -13,6 +13,8 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
+nextflow.enable.types = true
+
 process FASTA_SPLIT {
     tag "${meta.id}"
     label 'process_medium'
@@ -21,12 +23,17 @@ process FASTA_SPLIT {
     container "docker.io/ensemblorg/ensembl-genomio:v1.7.0"
 
     input:
-        tuple val(meta), path(fasta), val(longest_seq_bp)
+        record(meta: Map, fasta: Path, longest_seq_bp: Integer)
 
     output:
-        tuple val(meta), path("splits/**/*.fa"), emit: fastas
-        tuple val(meta), path("splits/*.agp"), emit: agp, optional: true
-        tuple val("${task.process}"), val('fasta_split'), eval("fasta_split --version"), emit: versions_fasta_split, topic: versions
+        record(
+            meta: meta,
+            fastas: files("splits/**/*.fa"),
+            agp: file("splits/*.agp", optional: true)
+        )
+
+    topic:
+        tuple(task.process, 'fasta_split', eval("fasta_split --version 2>/dev/null || echo unknown")) >> 'versions'
 
     when:
         task.ext.when == null || task.ext.when
diff --git a/modules/ensembl/fasta/split/meta.yml b/modules/ensembl/fasta/split/meta.yml
index 1e10f3a..ec2c04b 100644
--- a/modules/ensembl/fasta/split/meta.yml
+++ b/modules/ensembl/fasta/split/meta.yml
@@ -55,16 +55,6 @@ output:
           pattern: "splits/*.agp"
           ontologies:
             - edam: "http://edamontology.org/format_3693" # AGP
-  versions_fasta_split:
-    - - ${task.process}:
-          type: string
-          description: The name of the process.
-      - fasta_split:
-          type: string
-          description: The name of the tool.
-      - "fasta_split --version":
-          type: eval
-          description: The expression to obtain the version of the tool
 topics:
   versions:
     - - ${task.process}:
@@ -73,7 +63,7 @@ topics:
       - fasta_split:
           type: string
           description: The name of the tool.
-      - "fasta_split --version":
+      - "fasta_split --version 2>/dev/null || echo unknown":
           type: eval
           description: The expression to obtain the version of the tool
 authors:
diff --git a/modules/ensembl/fasta/split/tests/main.nf.test b/modules/ensembl/fasta/split/tests/main.nf.test
index 79d4c07..7c3b40d 100644
--- a/modules/ensembl/fasta/split/tests/main.nf.test
+++ b/modules/ensembl/fasta/split/tests/main.nf.test
@@ -24,6 +24,7 @@ nextflow_process {
     tag "modules_ensembl"
     tag "fasta"
     tag "fasta/split"
+    topics "versions"
 
 
     test("stub outputs: default layout, no AGP") {
@@ -38,28 +39,33 @@ nextflow_process {
 
             process {
                 """
-                input[0] = [[ id:'test' ], file('dummy.fa'), 1000]
+                input[0] = record(meta: [ id:'test' ], fasta: file('dummy.fa'), longest_seq_bp: 1000)
                 """
             }
         }
 
         then {
-            assert snapshot(process.out).match()
+            assert snapshot(
+                process.out[0].collect { output -> [ meta: output.meta, fastas: output.fastas.collect { path(it).toFile().name }.sort(), agp: output.agp ] },
+                topics.versions
+            ).match()
 
-            assert process.out.fastas != null
-            assert process.out.fastas.size() == 1
+            assert process.out[0] != null
+            assert process.out[0].size() == 1
 
-            def fasta_out = process.out.fastas[0]
-            def meta = fasta_out[0]
-            def fas  = fasta_out[1]
+            def fasta_out = process.out[0][0]
+            def meta = fasta_out.meta
+            def fas  = fasta_out.fastas
 
             assert meta.id == "test"
             assert fas != null
             assert fas.size() == 2
             assert fas.collect { path(it).toFile().name }.sort() == ["test.1.fa", "test.2.fa"]
 
-            assert process.out.agp != null
-            assert process.out.agp.size() == 0
+            assert process.out[0][0].agp == null
+            assert topics.versions.size() == 1
+            assert topics.versions[0].size() == 3
+            assert topics.versions[0][0] == 'FASTA_SPLIT'
 
             assertAll(
                 { assert process.success }
@@ -79,23 +85,25 @@ nextflow_process {
 
             process {
                 """
-                input[0] = [[ id:'test' ], file('dummy.fa'), 1000]
+                input[0] = record(meta: [ id:'test' ], fasta: file('dummy.fa'), longest_seq_bp: 1000)
                 """
             }
         }
 
         then {
-            assert snapshot(process.out).match()
-
-            assert process.out.fastas.size() == 1
-            def fasta_out = process.out.fastas[0]
-            def fas = fasta_out[1]
+            assert snapshot(
+                process.out[0].collect { output -> [ meta: output.meta, fastas: output.fastas.collect { path(it).toFile().name }.sort(), agp: output.agp ] },
+                topics.versions
+            ).match()
+
+            assert process.out[0].size() == 1
+            def fasta_out = process.out[0][0]
+            def fas = fasta_out.fastas
             assert fas.size() == 2
 
-            assert process.out.agp.size() == 1
-            def agp_out = process.out.agp[0]
-            def agp_meta = agp_out[0]
-            def agp = agp_out[1]
+            def agp_out = process.out[0][0]
+            def agp_meta = agp_out.meta
+            def agp = agp_out.agp
             def agp_paths = agp instanceof List ? agp : [agp]
             def agp_file = path(agp_paths[0]).toFile()
 
@@ -121,19 +129,22 @@ nextflow_process {
 
             process {
                 """
-                input[0] = [[ id:'test' ], file('dummy.fa'), 1000]
+                input[0] = record(meta: [ id:'test' ], fasta: file('dummy.fa'), longest_seq_bp: 1000)
                 """
             }
         }
 
         then {
-            assert snapshot(process.out).match()
+            assert snapshot(
+                process.out[0].collect { output -> [ meta: output.meta, fastas: output.fastas.collect { path(it).toFile().name }.sort(), agp: output.agp ] },
+                topics.versions
+            ).match()
 
-            def fasta_out = process.out.fastas[0]
-            def fas = fasta_out[1]
+            def fasta_out = process.out[0][0]
+            def fas = fasta_out.fastas
 
             assert fas.size() == 2
-            assert process.out.agp.size() == 0
+            assert process.out[0][0].agp == null
 
             // Contract check: names match the unique fixture pattern
             assert fas.collect { path(it).toFile().name }.sort() == ["test.0.1.fa", "test.0.2.fa"]
@@ -158,17 +169,20 @@ nextflow_process {
 
             process {
                 """
-                input[0] = [[ id:'test' ], file('dummy.fa'), 1000]
+                input[0] = record(meta: [ id:'test' ], fasta: file('dummy.fa'), longest_seq_bp: 1000)
                 """
             }
         }
 
         then {
-            assert snapshot(process.out).match()
+            assert snapshot(
+                process.out[0].collect { output -> [ meta: output.meta, fastas: output.fastas.collect { path(it).toFile().name }.sort(), agp: output.agp ] },
+                topics.versions
+            ).match()
 
-            def fastas = process.out.fastas[0][1]
+            def fastas = process.out[0][0].fastas
             assert fastas.size() == 2
-            assert process.out.agp.size() == 0
+            assert process.out[0][0].agp == null
 
             def rels = fastas.collect { path(it).toString() }
             assert rels.any { it.contains("splits/0/0/") }
diff --git a/modules/ensembl/fasta/split/tests/main.nf.test.snap b/modules/ensembl/fasta/split/tests/main.nf.test.snap
index d35b001..d3327c3 100644
--- a/modules/ensembl/fasta/split/tests/main.nf.test.snap
+++ b/modules/ensembl/fasta/split/tests/main.nf.test.snap
@@ -1,224 +1,114 @@
 {
     "stub outputs: default layout, no AGP": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "test.1.fa:md5,9470e6594eeaecc474f45f1dbcc040bd",
-                            "test.2.fa:md5,9470e6594eeaecc474f45f1dbcc040bd"
-                        ]
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    [
-                        "FASTA_SPLIT",
-                        "fasta_split",
-                        "1.7.0"
-                    ]
-                ],
-                "agp": [
-                    
-                ],
-                "fastas": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "test.1.fa:md5,9470e6594eeaecc474f45f1dbcc040bd",
-                            "test.2.fa:md5,9470e6594eeaecc474f45f1dbcc040bd"
-                        ]
-                    ]
-                ],
-                "versions_fasta_split": [
-                    [
-                        "FASTA_SPLIT",
-                        "fasta_split",
-                        "1.7.0"
-                    ]
+            [
+                {
+                    "meta": {
+                        "id": "test"
+                    },
+                    "fastas": [
+                        "test.1.fa",
+                        "test.2.fa"
+                    ],
+                    "agp": null
+                }
+            ],
+            [
+                [
+                    "FASTA_SPLIT",
+                    "fasta_split",
+                    "1.7.0"
                 ]
-            }
+            ]
         ],
-        "timestamp": "2026-06-11T18:08:56.777146",
+        "timestamp": "2026-09-29T12:58:12.875276",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "stub outputs: AGP optional output appears when enabled": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "test.1.fa:md5,9470e6594eeaecc474f45f1dbcc040bd",
-                            "test.2.fa:md5,9470e6594eeaecc474f45f1dbcc040bd"
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.agp:md5,38e242a83da3c6d49933988b89ac1ed8"
-                    ]
-                ],
-                "2": [
-                    [
-                        "FASTA_SPLIT",
-                        "fasta_split",
-                        "1.7.0"
-                    ]
-                ],
-                "agp": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.agp:md5,38e242a83da3c6d49933988b89ac1ed8"
-                    ]
-                ],
-                "fastas": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "test.1.fa:md5,9470e6594eeaecc474f45f1dbcc040bd",
-                            "test.2.fa:md5,9470e6594eeaecc474f45f1dbcc040bd"
-                        ]
-                    ]
-                ],
-                "versions_fasta_split": [
-                    [
-                        "FASTA_SPLIT",
-                        "fasta_split",
-                        "1.7.0"
-                    ]
+            [
+                {
+                    "meta": {
+                        "id": "test"
+                    },
+                    "fastas": [
+                        "test.1.fa",
+                        "test.2.fa"
+                    ],
+                    "agp": "test.agp:md5,38e242a83da3c6d49933988b89ac1ed8"
+                }
+            ],
+            [
+                [
+                    "FASTA_SPLIT",
+                    "fasta_split",
+                    "1.7.0"
                 ]
-            }
+            ]
         ],
-        "timestamp": "2026-06-11T18:08:59.155435",
+        "timestamp": "2026-09-29T12:58:15.411763",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "stub outputs: nested directory layout contract": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "test.1.fa:md5,9470e6594eeaecc474f45f1dbcc040bd",
-                            "test.2.fa:md5,9470e6594eeaecc474f45f1dbcc040bd"
-                        ]
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    [
-                        "FASTA_SPLIT",
-                        "fasta_split",
-                        "1.7.0"
-                    ]
-                ],
-                "agp": [
-                    
-                ],
-                "fastas": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "test.1.fa:md5,9470e6594eeaecc474f45f1dbcc040bd",
-                            "test.2.fa:md5,9470e6594eeaecc474f45f1dbcc040bd"
-                        ]
-                    ]
-                ],
-                "versions_fasta_split": [
-                    [
-                        "FASTA_SPLIT",
-                        "fasta_split",
-                        "1.7.0"
-                    ]
+            [
+                {
+                    "meta": {
+                        "id": "test"
+                    },
+                    "fastas": [
+                        "test.1.fa",
+                        "test.2.fa"
+                    ],
+                    "agp": null
+                }
+            ],
+            [
+                [
+                    "FASTA_SPLIT",
+                    "fasta_split",
+                    "1.7.0"
                 ]
-            }
+            ]
         ],
-        "timestamp": "2026-06-11T18:09:03.870638",
+        "timestamp": "2026-09-29T12:58:20.662075",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "stub outputs: unique_file_names contract": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "test.0.1.fa:md5,9470e6594eeaecc474f45f1dbcc040bd",
-                            "test.0.2.fa:md5,9470e6594eeaecc474f45f1dbcc040bd"
-                        ]
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    [
-                        "FASTA_SPLIT",
-                        "fasta_split",
-                        "1.7.0"
-                    ]
-                ],
-                "agp": [
-                    
-                ],
-                "fastas": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "test.0.1.fa:md5,9470e6594eeaecc474f45f1dbcc040bd",
-                            "test.0.2.fa:md5,9470e6594eeaecc474f45f1dbcc040bd"
-                        ]
-                    ]
-                ],
-                "versions_fasta_split": [
-                    [
-                        "FASTA_SPLIT",
-                        "fasta_split",
-                        "1.7.0"
-                    ]
+            [
+                {
+                    "meta": {
+                        "id": "test"
+                    },
+                    "fastas": [
+                        "test.0.1.fa",
+                        "test.0.2.fa"
+                    ],
+                    "agp": null
+                }
+            ],
+            [
+                [
+                    "FASTA_SPLIT",
+                    "fasta_split",
+                    "1.7.0"
                 ]
-            }
+            ]
         ],
-        "timestamp": "2026-06-11T18:09:01.510794",
+        "timestamp": "2026-09-29T12:58:17.991847",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     }
-}
\ No newline at end of file
+}
diff --git a/modules/ensembl/fasta/stats/main.nf b/modules/ensembl/fasta/stats/main.nf
index 94c404f..3456982 100644
--- a/modules/ensembl/fasta/stats/main.nf
+++ b/modules/ensembl/fasta/stats/main.nf
@@ -13,6 +13,8 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
+nextflow.enable.types = true
+
 process FASTA_STATS {
 
     tag "${meta.id}"
@@ -22,11 +24,13 @@ process FASTA_STATS {
     container "docker.io/ensemblorg/ensembl-genomio:v1.7.0"
 
     input:
-        tuple val(meta), path(fasta)
+        record(meta: Map, fasta: Path)
 
     output:
-        tuple val(meta), path("${fasta.simpleName}.stats.json"), emit: stats
-        tuple val("${task.process}"), val('fasta_stats'), eval("fasta_stats --version"), emit: versions_fasta_stats, topic: versions
+        record(meta: meta, stats: file("${fasta.simpleName}.stats.json"))
+
+    topic:
+        tuple(task.process, 'fasta_stats', eval("fasta_stats --version 2>/dev/null || echo unknown")) >> 'versions'
 
     script:
         """
diff --git a/modules/ensembl/fasta/stats/meta.yml b/modules/ensembl/fasta/stats/meta.yml
index 608ec4b..f5dcb25 100644
--- a/modules/ensembl/fasta/stats/meta.yml
+++ b/modules/ensembl/fasta/stats/meta.yml
@@ -13,22 +13,23 @@ authors:
   - "ensembl-dev@ebi.ac.uk"
 
 input:
-  - meta:
-      type: map
-      description: Groovy meta map
-  - fasta:
-      type: file
-      description: FASTA file
-      pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}"
+  - - meta:
+        type: map
+        description: Groovy meta map
+    - fasta:
+        type: file
+        description: FASTA file
+        pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}"
 
 output:
-  - meta:
-      type: map
-      description: Groovy meta map
-  - stats:
-      type: file
-      description: JSON file containing FASTA statistics
-      pattern: "*.stats.json"
+  stats:
+    - - meta:
+          type: map
+          description: Groovy meta map
+      - stats:
+          type: file
+          description: JSON file containing FASTA statistics
+          pattern: "*.stats.json"
 
 topics:
   versions:
@@ -38,6 +39,6 @@ topics:
       - fasta_stats:
           type: string
           description: The name of the tool.
-      - ? fasta_stats --version
+      - ? fasta_stats --version 2>/dev/null || echo unknown
         : type: eval
-          description: The expression to obtain the version of the tool
\ No newline at end of file
+          description: The expression to obtain the version of the tool
diff --git a/modules/ensembl/fasta/stats/tests/main.nf.test b/modules/ensembl/fasta/stats/tests/main.nf.test
index f31bcb2..8e60b7e 100644
--- a/modules/ensembl/fasta/stats/tests/main.nf.test
+++ b/modules/ensembl/fasta/stats/tests/main.nf.test
@@ -23,6 +23,7 @@ nextflow_process {
     tag "modules_local"
     tag "fasta"
     tag "fasta/stats"
+    topics "versions"
 
     test("Stub outputs stats tuple and versions") {
 
@@ -33,7 +34,7 @@ nextflow_process {
                 """
                 def fasta = file("input.fa")
 
-                input[0] = [[ id:'test' ], fasta]
+                input[0] = record(meta: [ id:'test' ], fasta: fasta)
                 """
             }
         }
@@ -41,11 +42,14 @@ nextflow_process {
         then {
             assert process.success
             assert process.trace.tasks().size() == 1
-            assert process.out.stats.size() == 1
+            assert process.out[0].size() == 1
             
-            def stats_out = process.out.stats[0]
-            assert stats_out[0].id == "test"
-            assert file(stats_out[1]).name == "input.stats.json"
+            def stats_out = process.out[0][0]
+            assert stats_out.meta.id == "test"
+            assert file(stats_out.stats).name == "input.stats.json"
+            assert topics.versions.size() == 1
+            assert topics.versions[0].size() == 3
+            assert topics.versions[0][0] == 'FASTA_STATS'
             assert snapshot(process.out).match()
         }
     }
diff --git a/modules/ensembl/fasta/stats/tests/main.nf.test.snap b/modules/ensembl/fasta/stats/tests/main.nf.test.snap
index 8bb9783..e2bbf56 100644
--- a/modules/ensembl/fasta/stats/tests/main.nf.test.snap
+++ b/modules/ensembl/fasta/stats/tests/main.nf.test.snap
@@ -3,38 +3,16 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
+                    {
+                        "meta": {
                             "id": "test"
                         },
-                        "input.stats.json:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        "FASTA_STATS",
-                        "fasta_stats",
-                        "1.7.0"
-                    ]
-                ],
-                "stats": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "input.stats.json:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions_fasta_stats": [
-                    [
-                        "FASTA_STATS",
-                        "fasta_stats",
-                        "1.7.0"
-                    ]
+                        "stats": "input.stats.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-06-17T21:16:28.217339",
+        "timestamp": "2026-09-29T12:53:55.741606",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"
diff --git a/modules/ensembl/features/combine_json/main.nf b/modules/ensembl/features/combine_json/main.nf
index 2ffe177..1ec1033 100644
--- a/modules/ensembl/features/combine_json/main.nf
+++ b/modules/ensembl/features/combine_json/main.nf
@@ -13,6 +13,8 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
+nextflow.enable.types = true
+
 process FEATURES_COMBINE_JSON {
     tag "${meta.id}"
     label 'process_medium'
@@ -21,11 +23,18 @@ process FEATURES_COMBINE_JSON {
     container "docker.io/ensemblorg/ensembl-genomio:v1.7.0"
 
     input:
-        tuple val(meta), val(analysis), path(json_manifest), path(agp)
+        record(
+            meta: Map,
+            analysis: String,
+            json_manifest: Path,
+            agp: Path?
+        )
 
     output:
-        tuple val(meta), path("${meta.id}.${analysis}.json"), emit: combined_json
-        tuple val("${task.process}"), val('features_combine_json'), eval("features_combine_json --version"), emit: versions_features_combine_json, topic: versions
+        record(meta: meta, combined_json: file("${meta.id}.${analysis}.json"))
+
+    topic:
+        tuple(task.process, 'features_combine_json', eval("features_combine_json --version 2>/dev/null || echo unknown")) >> 'versions'
 
     when:
         task.ext.when == null || task.ext.when
diff --git a/modules/ensembl/features/combine_json/meta.yml b/modules/ensembl/features/combine_json/meta.yml
index 90a7b78..461904a 100644
--- a/modules/ensembl/features/combine_json/meta.yml
+++ b/modules/ensembl/features/combine_json/meta.yml
@@ -49,16 +49,6 @@ output:
           pattern: "*.json"
           ontologies:
             - edam: http://edamontology.org/format_3464 # JSON
-  versions_features_combine_json:
-    - - ${task.process}:
-          type: string
-          description: The name of the process.
-      - features_combine_json:
-          type: string
-          description: The name of the tool.
-      - "features_combine_json --version":
-          type: eval
-          description: The expression to obtain the version of the tool
 topics:
   versions:
     - - ${task.process}:
@@ -67,7 +57,7 @@ topics:
       - features_combine_json:
           type: string
           description: The name of the tool.
-      - "features_combine_json --version":
+      - "features_combine_json --version 2>/dev/null || echo unknown":
           type: eval
           description: The expression to obtain the version of the tool
 authors:
diff --git a/modules/ensembl/features/combine_json/tests/main.nf.test b/modules/ensembl/features/combine_json/tests/main.nf.test
index e4bc969..a203f50 100644
--- a/modules/ensembl/features/combine_json/tests/main.nf.test
+++ b/modules/ensembl/features/combine_json/tests/main.nf.test
@@ -24,6 +24,7 @@ nextflow_process {
     tag "modules_ensembl"
     tag "features"
     tag "features/combine_json"
+    topics "versions"
 
     test("Stub outputs") {
 
@@ -38,19 +39,23 @@ nextflow_process {
                 def noFile = file("NO_FILE")
                 noFile.text = ""
 
-                input[0] = [
-                    [ id:'test' ],
-                    'features',
-                    manifest,
-                    noFile
-                ]
+                input[0] = record(
+                    meta: [ id:'test' ],
+                    analysis: 'features',
+                    json_manifest: manifest,
+                    agp: noFile
+                )
                 """
             }
         }
 
         then {
             assert process.trace.tasks().size() == 1
-            assert process.out.combined_json.size() == 1
+            assert process.out[0].size() == 1
+            assert file(process.out[0][0].combined_json).name == 'test.features.json'
+            assert topics.versions.size() == 1
+            assert topics.versions[0].size() == 3
+            assert topics.versions[0][0] == 'FEATURES_COMBINE_JSON'
             assert process.success
             assert snapshot(process.out).match()
         }
diff --git a/modules/ensembl/features/combine_json/tests/main.nf.test.snap b/modules/ensembl/features/combine_json/tests/main.nf.test.snap
index c96b73a..795b77f 100644
--- a/modules/ensembl/features/combine_json/tests/main.nf.test.snap
+++ b/modules/ensembl/features/combine_json/tests/main.nf.test.snap
@@ -3,41 +3,19 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
+                    {
+                        "combined_json": "test.features.json:md5,8a80554c91d9fca8acb82f023de02f11",
+                        "meta": {
                             "id": "test"
-                        },
-                        "test.features.json:md5,8a80554c91d9fca8acb82f023de02f11"
-                    ]
-                ],
-                "1": [
-                    [
-                        "FEATURES_COMBINE_JSON",
-                        "features_combine_json",
-                        "1.7.0"
-                    ]
-                ],
-                "combined_json": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.features.json:md5,8a80554c91d9fca8acb82f023de02f11"
-                    ]
-                ],
-                "versions_features_combine_json": [
-                    [
-                        "FEATURES_COMBINE_JSON",
-                        "features_combine_json",
-                        "1.7.0"
-                    ]
+                        }
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-06-11T18:09:19.997741",
+        "timestamp": "2026-09-29T12:53:58.29327",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/ensembl/features/convert_to_json/main.nf b/modules/ensembl/features/convert_to_json/main.nf
index 12459f9..daa640a 100644
--- a/modules/ensembl/features/convert_to_json/main.nf
+++ b/modules/ensembl/features/convert_to_json/main.nf
@@ -13,22 +13,30 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
+nextflow.enable.types = true
+
 process FEATURES_CONVERT_TO_JSON {
     tag "${meta.id}"
     label 'process_small'
     container 'docker.io/ensemblorg/ensembl-genomio:v1.7.0'
 
     input:
-        tuple val(meta), path(features_out), path(repeatmasker_consensus_lib)
-        val(analysis_logic_name)
-        val(program_version)
-        val(program_parameters)
-        val(annotation_provider)
-        val(is_primary_source)
+        record(
+            meta: Map,
+            features_out: Path,
+            repeatmasker_consensus_lib: Path?,
+            analysis_logic_name: String,
+            program_version: String,
+            program_parameters: String?,
+            annotation_provider: String?,
+            is_primary_source: Boolean
+        )
 
     output:
-        tuple val(meta), path("${meta.id}.${analysis_logic_name}.features.json"), emit: features_json
-        tuple val("${task.process}"), val('features_convert_to_genomio_json'), eval("features_convert_to_genomio_json --version"), emit: versions_convert_to_genomio_json, topic: versions
+        record(meta: meta, features_json: file("${meta.id}.${analysis_logic_name}.features.json"))
+
+    topic:
+        tuple(task.process, 'features_convert_to_genomio_json', eval("features_convert_to_genomio_json --version 2>/dev/null || echo unknown")) >> 'versions'
 
     script:
         def prefix = ''
@@ -70,4 +78,4 @@ process FEATURES_CONVERT_TO_JSON {
         {}
         EOF
         """
-}
\ No newline at end of file
+}
diff --git a/modules/ensembl/features/convert_to_json/meta.yml b/modules/ensembl/features/convert_to_json/meta.yml
index a8c568a..3286125 100644
--- a/modules/ensembl/features/convert_to_json/meta.yml
+++ b/modules/ensembl/features/convert_to_json/meta.yml
@@ -62,7 +62,7 @@ input:
       type: boolean
       description: Whether the annotation provider is the primary source.
 output:
-  json:
+  features_json:
     - - meta:
           type: map
           description: |
@@ -74,25 +74,15 @@ output:
           pattern: "*.features.json"
           ontologies:
             - edam: http://edamontology.org/format_3464
-  versions_features_convert_to_json:
-    - - ${task.process}:
-          type: string
-          description: The name of the process.
-      - features_convert_to_json:
-          type: string
-          description: The name of the tool.
-      - ? features_convert_to_json --version
-        : type: eval
-          description: The expression to obtain the version of the tool
 topics:
   versions:
     - - ${task.process}:
           type: string
           description: The name of the process.
-      - features_convert_to_json:
+      - features_convert_to_genomio_json:
           type: string
           description: The name of the tool.
-      - ? features_convert_to_json --version
+      - ? features_convert_to_genomio_json --version 2>/dev/null || echo unknown
         : type: eval
           description: The expression to obtain the version of the tool
 authors:
diff --git a/modules/ensembl/features/convert_to_json/tests/main.nf.test b/modules/ensembl/features/convert_to_json/tests/main.nf.test
index 8df097e..713c381 100644
--- a/modules/ensembl/features/convert_to_json/tests/main.nf.test
+++ b/modules/ensembl/features/convert_to_json/tests/main.nf.test
@@ -23,6 +23,7 @@ nextflow_process {
     tag "modules_local"
     tag "features"
     tag "features/convert_to_json"
+    topics "versions"
 
     test("Stub wires TRF input mode") {
 
@@ -37,26 +38,33 @@ nextflow_process {
                 def noFile = file("NO_FILE")
                 noFile.text = ""
 
-                input[0] = [[ id:'test' ], featuresOut, noFile]
-                input[1] = "trf"
-                input[2] = "4.1.7"
-                input[3] = "-species stub"
-                input[4] = "stub_provider"
-                input[5] = false
+                input[0] = record(
+                    meta: [ id:'test' ],
+                    features_out: featuresOut,
+                    repeatmasker_consensus_lib: noFile,
+                    analysis_logic_name: 'trf',
+                    program_version: '4.1.7',
+                    program_parameters: '-species stub',
+                    annotation_provider: 'stub_provider',
+                    is_primary_source: false
+                )
                 """
             }
         }
 
         then {
             assert process.success
-            assert process.out.features_json.size() == 1
+            assert process.out[0].size() == 1
 
-            def jsonPath = process.out.features_json[0][1]
+            def jsonPath = process.out[0][0].features_json
             def jsonFile = path(jsonPath).toFile()
 
             assert jsonFile.exists()
             assert jsonFile.name == "test.trf.features.json"
-            assert process.out.features_json[0][0].id == "test"
+            assert process.out[0][0].meta.id == "test"
+            assert topics.versions.size() == 1
+            assert topics.versions[0].size() == 3
+            assert topics.versions[0][0] == 'FEATURES_CONVERT_TO_JSON'
             assert snapshot(process.out).match()
         }
     }
@@ -74,26 +82,33 @@ nextflow_process {
                 def noFile = file("NO_FILE")
                 noFile.text = ""
 
-                input[0] = [[ id:'test' ], featuresOut, noFile]
-                input[1] = "repeatmasker_repbase"
-                input[2] = "4.1.7"
-                input[3] = "-species stub"
-                input[4] = "stub_provider"
-                input[5] = false
+                input[0] = record(
+                    meta: [ id:'test' ],
+                    features_out: featuresOut,
+                    repeatmasker_consensus_lib: noFile,
+                    analysis_logic_name: 'repeatmasker_repbase',
+                    program_version: '4.1.7',
+                    program_parameters: '-species stub',
+                    annotation_provider: 'stub_provider',
+                    is_primary_source: false
+                )
                 """
             }
         }
 
         then {
             assert process.success
-            assert process.out.features_json.size() == 1
+            assert process.out[0].size() == 1
 
-            def jsonPath = process.out.features_json[0][1]
+            def jsonPath = process.out[0][0].features_json
             def jsonFile = path(jsonPath).toFile()
 
             assert jsonFile.exists()
             assert jsonFile.name == "test.repeatmasker_repbase.features.json"
-            assert process.out.features_json[0][0].id == "test"
+            assert process.out[0][0].meta.id == "test"
+            assert topics.versions.size() == 1
+            assert topics.versions[0].size() == 3
+            assert topics.versions[0][0] == 'FEATURES_CONVERT_TO_JSON'
             assert snapshot(process.out).match()
         }
     }
@@ -111,26 +126,33 @@ nextflow_process {
                 def consensus = file("repeatmodeler.fa")
                 consensus.text = ">consensus\\nACGT\\n"
 
-                input[0] = [[ id:'test' ], featuresOut, consensus]
-                input[1] = "repeatmask_customlib"
-                input[2] = "4.1.7"
-                input[3] = "-species stub"
-                input[4] = "stub_provider"
-                input[5] = true
+                input[0] = record(
+                    meta: [ id:'test' ],
+                    features_out: featuresOut,
+                    repeatmasker_consensus_lib: consensus,
+                    analysis_logic_name: 'repeatmask_customlib',
+                    program_version: '4.1.7',
+                    program_parameters: '-species stub',
+                    annotation_provider: 'stub_provider',
+                    is_primary_source: true
+                )
                 """
             }
         }
 
         then {
             assert process.success
-            assert process.out.features_json.size() == 1
+            assert process.out[0].size() == 1
 
-            def jsonPath = process.out.features_json[0][1]
+            def jsonPath = process.out[0][0].features_json
             def jsonFile = path(jsonPath).toFile()
 
             assert jsonFile.exists()
             assert jsonFile.name == "test.repeatmask_customlib.features.json"
-            assert process.out.features_json[0][0].id == "test"
+            assert process.out[0][0].meta.id == "test"
+            assert topics.versions.size() == 1
+            assert topics.versions[0].size() == 3
+            assert topics.versions[0][0] == 'FEATURES_CONVERT_TO_JSON'
             assert snapshot(process.out).match()
         }
     }
diff --git a/modules/ensembl/features/convert_to_json/tests/main.nf.test.snap b/modules/ensembl/features/convert_to_json/tests/main.nf.test.snap
index 464cbd9..0dc7c07 100644
--- a/modules/ensembl/features/convert_to_json/tests/main.nf.test.snap
+++ b/modules/ensembl/features/convert_to_json/tests/main.nf.test.snap
@@ -3,38 +3,16 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
+                    {
+                        "features_json": "test.repeatmask_customlib.features.json:md5,8a80554c91d9fca8acb82f023de02f11",
+                        "meta": {
                             "id": "test"
-                        },
-                        "test.repeatmask_customlib.features.json:md5,8a80554c91d9fca8acb82f023de02f11"
-                    ]
-                ],
-                "1": [
-                    [
-                        "FEATURES_CONVERT_TO_JSON",
-                        "features_convert_to_genomio_json",
-                        "1.7.0"
-                    ]
-                ],
-                "features_json": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.repeatmask_customlib.features.json:md5,8a80554c91d9fca8acb82f023de02f11"
-                    ]
-                ],
-                "versions_convert_to_genomio_json": [
-                    [
-                        "FEATURES_CONVERT_TO_JSON",
-                        "features_convert_to_genomio_json",
-                        "1.7.0"
-                    ]
+                        }
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-06-23T11:49:16.328488",
+        "timestamp": "2026-09-29T12:54:04.437296",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"
@@ -44,38 +22,16 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.repeatmasker_repbase.features.json:md5,8a80554c91d9fca8acb82f023de02f11"
-                    ]
-                ],
-                "1": [
-                    [
-                        "FEATURES_CONVERT_TO_JSON",
-                        "features_convert_to_genomio_json",
-                        "1.7.0"
-                    ]
-                ],
-                "features_json": [
-                    [
-                        {
+                    {
+                        "features_json": "test.repeatmasker_repbase.features.json:md5,8a80554c91d9fca8acb82f023de02f11",
+                        "meta": {
                             "id": "test"
-                        },
-                        "test.repeatmasker_repbase.features.json:md5,8a80554c91d9fca8acb82f023de02f11"
-                    ]
-                ],
-                "versions_convert_to_genomio_json": [
-                    [
-                        "FEATURES_CONVERT_TO_JSON",
-                        "features_convert_to_genomio_json",
-                        "1.7.0"
-                    ]
+                        }
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-06-23T11:49:13.92402",
+        "timestamp": "2026-09-29T12:54:02.363885",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"
@@ -85,38 +41,16 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.trf.features.json:md5,8a80554c91d9fca8acb82f023de02f11"
-                    ]
-                ],
-                "1": [
-                    [
-                        "FEATURES_CONVERT_TO_JSON",
-                        "features_convert_to_genomio_json",
-                        "1.7.0"
-                    ]
-                ],
-                "features_json": [
-                    [
-                        {
+                    {
+                        "features_json": "test.trf.features.json:md5,8a80554c91d9fca8acb82f023de02f11",
+                        "meta": {
                             "id": "test"
-                        },
-                        "test.trf.features.json:md5,8a80554c91d9fca8acb82f023de02f11"
-                    ]
-                ],
-                "versions_convert_to_genomio_json": [
-                    [
-                        "FEATURES_CONVERT_TO_JSON",
-                        "features_convert_to_genomio_json",
-                        "1.7.0"
-                    ]
+                        }
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-06-23T11:49:11.562335",
+        "timestamp": "2026-09-29T12:54:00.329076",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"
diff --git a/modules/ensembl/features/red/main.nf b/modules/ensembl/features/red/main.nf
index 063ffa1..5e378d1 100644
--- a/modules/ensembl/features/red/main.nf
+++ b/modules/ensembl/features/red/main.nf
@@ -13,6 +13,8 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
+nextflow.enable.types = true
+
 process FEATURES_RED {
     tag "${meta.id}"
     label 'process_medium'
@@ -21,11 +23,13 @@ process FEATURES_RED {
     container "quay.io/biocontainers/red:2018.09.10--h9948957_3"
 
     input:
-        tuple val(meta), path(fasta)
+        record(meta: Map, fasta: Path)
 
     output:
-        tuple val(meta), path("rpt/*.bed"), emit: bed
-        tuple val("${task.process}"), val('red'), eval("conda list red --json | python -c 'import sys,json; print(json.load(sys.stdin)[0][\"version\"])' || echo 2.0"), emit: versions_red, topic: versions
+        record(meta: meta, bed: file("rpt/*.bed"))
+
+    topic:
+        tuple(task.process, 'red', eval("conda list red --json | python -c 'import sys,json; print(json.load(sys.stdin)[0][\"version\"])' || echo 2.0")) >> 'versions'
 
     when:
         task.ext.when == null || task.ext.when
diff --git a/modules/ensembl/features/red/meta.yml b/modules/ensembl/features/red/meta.yml
index 93d1319..05452dc 100644
--- a/modules/ensembl/features/red/meta.yml
+++ b/modules/ensembl/features/red/meta.yml
@@ -30,7 +30,7 @@ input:
         ontologies:
           - edam: "http://edamontology.org/format_1929" # FASTA
 output:
-  rpt:
+  bed:
     - - meta:
           type: map
           description: |
@@ -40,16 +40,6 @@ output:
           type: file
           description: Red repeat report file.
           pattern: "*.bed"
-  versions_red:
-    - - ${task.process}:
-          type: string
-          description: The process the versions were collected from
-      - red:
-          type: string
-          description: The tool name
-      - conda list red --json | python -c 'import sys,json; print(json.load(sys.stdin)[0]["version"])' || echo 2.0:
-          type: eval
-          description: The expression to obtain the Red version
 topics:
   versions:
     - - ${task.process}:
diff --git a/modules/ensembl/features/red/tests/main.nf.test b/modules/ensembl/features/red/tests/main.nf.test
index 0371ef2..946bef0 100644
--- a/modules/ensembl/features/red/tests/main.nf.test
+++ b/modules/ensembl/features/red/tests/main.nf.test
@@ -23,6 +23,7 @@ nextflow_process {
     tag "modules_local"
     tag "features"
     tag "features/red"
+    topics "versions"
 
     test("Stub creates Red repeat report") {
 
@@ -34,7 +35,7 @@ nextflow_process {
                 def fasta = file("test.fa")
                 fasta.text = ">test\\nACGT\\n"
 
-                input[0] = [[ id:'test' ], fasta]
+                input[0] = record(meta: [ id:'test' ], fasta: fasta)
                 """
             }
         }
@@ -42,11 +43,13 @@ nextflow_process {
         then {
             assert process.success
             assert snapshot(process.out).match()
-            assert process.out.bed.size() == 1
-            assert process.out.bed[0][0] == [ id: 'test' ]
-            assert file(process.out.bed[0][1]).name == "test.bed"
-            assert file(process.out.bed[0][1]).size() > 0
-            assert process.out.versions_red.size() == 1
+            assert process.out[0].size() == 1
+            assert process.out[0][0].meta == [ id: 'test' ]
+            assert file(process.out[0][0].bed).name == "test.bed"
+            assert file(process.out[0][0].bed).size() > 0
+            assert topics.versions.size() == 1
+            assert topics.versions[0].size() == 3
+            assert topics.versions[0][0] == 'FEATURES_RED'
         }
     }
 }
diff --git a/modules/ensembl/features/red/tests/main.nf.test.snap b/modules/ensembl/features/red/tests/main.nf.test.snap
index 3414eb0..7648c3c 100644
--- a/modules/ensembl/features/red/tests/main.nf.test.snap
+++ b/modules/ensembl/features/red/tests/main.nf.test.snap
@@ -3,38 +3,16 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
+                    {
+                        "bed": "test.bed:md5,aa604b48150afc506072a1f9656b6bb7",
+                        "meta": {
                             "id": "test"
-                        },
-                        "test.bed:md5,aa604b48150afc506072a1f9656b6bb7"
-                    ]
-                ],
-                "1": [
-                    [
-                        "FEATURES_RED",
-                        "red",
-                        "2.0"
-                    ]
-                ],
-                "bed": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,aa604b48150afc506072a1f9656b6bb7"
-                    ]
-                ],
-                "versions_red": [
-                    [
-                        "FEATURES_RED",
-                        "red",
-                        "2.0"
-                    ]
+                        }
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-07-14T16:03:16.866216",
+        "timestamp": "2026-09-29T12:54:06.783701",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"
diff --git a/modules/ensembl/features/trf/main.nf b/modules/ensembl/features/trf/main.nf
index 475dba6..55267c0 100644
--- a/modules/ensembl/features/trf/main.nf
+++ b/modules/ensembl/features/trf/main.nf
@@ -13,6 +13,8 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
+nextflow.enable.types = true
+
 process FEATURES_TRF {
     tag "${meta.id}"
     label 'process_medium'
@@ -21,11 +23,13 @@ process FEATURES_TRF {
     container "quay.io/biocontainers/trf:4.10.0rc2--h7b50bb2_0"
 
     input:
-        tuple val(meta), path(fasta)
+        record(meta: Map, fasta: Path)
 
     output:
-        tuple val(meta), path("*.dat"), emit: dat
-        tuple val("${task.process}"), val('trf'), eval("trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0"), emit: versions_trf, topic: versions
+        record(meta: meta, dat: file("*.dat"))
+
+    topic:
+        tuple(task.process, 'trf', eval("trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0")) >> 'versions'
 
     when:
         task.ext.when == null || task.ext.when
diff --git a/modules/ensembl/features/trf/meta.yml b/modules/ensembl/features/trf/meta.yml
index 043433c..0855ac9 100644
--- a/modules/ensembl/features/trf/meta.yml
+++ b/modules/ensembl/features/trf/meta.yml
@@ -39,16 +39,6 @@ output:
           type: file
           description: TRF repeat annotations in DAT format
           pattern: "*.dat"
-  versions_trf:
-    - - ${task.process}:
-          type: string
-          description: The process the versions were collected from
-      - trf:
-          type: string
-          description: The tool name
-      - trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0:
-          type: eval
-          description: The expression to obtain the TRF version
 topics:
   versions:
     - - ${task.process}:
diff --git a/modules/ensembl/features/trf/tests/main.nf.test b/modules/ensembl/features/trf/tests/main.nf.test
index 348c575..ff4721c 100644
--- a/modules/ensembl/features/trf/tests/main.nf.test
+++ b/modules/ensembl/features/trf/tests/main.nf.test
@@ -22,6 +22,7 @@ nextflow_process {
 
     tag "features"
     tag "features/trf"
+    topics "versions"
 
     test("Stub: TRF") {
         when {
@@ -29,8 +30,7 @@ nextflow_process {
 
             process {
                 """
-                input[0] = [[ id: 'test' ],file('dummy.fa')
-                ]
+                input[0] = record(meta: [ id: 'test' ], fasta: file('dummy.fa'))
                 """
             }
         }
@@ -38,11 +38,13 @@ nextflow_process {
         then {
             assert process.success
             assert snapshot(process.out).match()
-            assert process.out.dat.size() == 1
-            assert process.out.dat[0][0] == [ id: 'test' ]
-            assert file(process.out.dat[0][1]).name == 'dummy.fa.dat'
-            assert file(process.out.dat[0][1]).size() > 0
-            assert process.out.versions_trf.size() == 1
+            assert process.out[0].size() == 1
+            assert process.out[0][0].meta == [ id: 'test' ]
+            assert file(process.out[0][0].dat).name == 'dummy.fa.dat'
+            assert file(process.out[0][0].dat).size() > 0
+            assert topics.versions.size() == 1
+            assert topics.versions[0].size() == 3
+            assert topics.versions[0][0] == 'FEATURES_TRF'
         }
     }
 }
diff --git a/modules/ensembl/features/trf/tests/main.nf.test.snap b/modules/ensembl/features/trf/tests/main.nf.test.snap
index 7325e37..92300cd 100644
--- a/modules/ensembl/features/trf/tests/main.nf.test.snap
+++ b/modules/ensembl/features/trf/tests/main.nf.test.snap
@@ -3,38 +3,16 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
+                    {
+                        "dat": "dummy.fa.dat:md5,7afa5cc8da76212b28fe6a2c4db74917",
+                        "meta": {
                             "id": "test"
-                        },
-                        "dummy.fa.dat:md5,7afa5cc8da76212b28fe6a2c4db74917"
-                    ]
-                ],
-                "1": [
-                    [
-                        "FEATURES_TRF",
-                        "trf",
-                        "4.10.0"
-                    ]
-                ],
-                "dat": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "dummy.fa.dat:md5,7afa5cc8da76212b28fe6a2c4db74917"
-                    ]
-                ],
-                "versions_trf": [
-                    [
-                        "FEATURES_TRF",
-                        "trf",
-                        "4.10.0"
-                    ]
+                        }
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-06-25T13:50:41.590756",
+        "timestamp": "2026-09-29T12:54:08.817888",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"