diff --git a/.gitignore b/.gitignore
index e75900d..961b31c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,5 @@
 .nextflow*
 .nf-test*
+__pycache__/
+*.pyc
+.python-version
\ No newline at end of file
diff --git a/modules/ensembl/fasta/recombine/environment.yml b/modules/ensembl/fasta/recombine/environment.yml
new file mode 100644
index 0000000..94089f3
--- /dev/null
+++ b/modules/ensembl/fasta/recombine/environment.yml
@@ -0,0 +1,6 @@
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - ensembl-genomio=1.6.1
diff --git a/modules/ensembl/fasta/recombine/main.nf b/modules/ensembl/fasta/recombine/main.nf
new file mode 100644
index 0000000..d14d71b
--- /dev/null
+++ b/modules/ensembl/fasta/recombine/main.nf
@@ -0,0 +1,66 @@
+// See the NOTICE file distributed with this work for additional information
+// regarding copyright ownership.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+process FASTA_RECOMBINE {
+
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/ensembl-genomio:1.6.1--pyhdfd78af_0'
+        : 'quay.io/biocontainers/ensembl-genomio:1.6.1--pyhdfd78af_0'}"
+
+    input:
+        tuple val(meta), path(fasta_manifest), path(agp)
+
+    output:
+        tuple val(meta), path("${meta.id}.fa"), emit: recombined_fasta
+        tuple val("${task.process}"), val('fasta_recombine'), eval("fasta_recombine --version"), emit: versions_fasta_recombine, topic: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = []
+
+        if (params.chunk_id_regex) {
+            def rx = params.chunk_id_regex.replace("'", "'\"'\"'")
+            args << "--chunk-id-regex '${rx}'"
+        }
+
+        if (params.allow_revcomp) {
+            args << "--allow-revcomp"
+        }
+
+        def has_agp = agp && agp.baseName != 'NO_FILE'
+        if (has_agp) {
+            args << "--agp-file ${agp}"
+        }
+
+        def out_fasta = "${meta.id}.fa"
+        """
+        fasta_recombine \\
+            --fasta-manifest ${fasta_manifest} \\
+            --out-fasta ${out_fasta} \\
+            ${args.join(' ')}
+        """
+
+    stub:
+        """
+        out_fa="${meta.id}.fa"
+        touch "\$out_fa"
+        """   
+}
diff --git a/modules/ensembl/fasta/recombine/meta.yml b/modules/ensembl/fasta/recombine/meta.yml
new file mode 100644
index 0000000..7c7aec4
--- /dev/null
+++ b/modules/ensembl/fasta/recombine/meta.yml
@@ -0,0 +1,71 @@
+name: "fasta_recombine"
+description: Recombine split FASTA sequences into a single FASTA file,
+  optionally using an AGP file.
+keywords:
+  - ensembl
+  - fasta
+  - genomics
+  - genomio
+  - recombine
+tools:
+  - "fasta_recombine":
+      description: "Recombine split FASTA sequences generated by ensembl-genomio."
+      homepage: "https://github.com/Ensembl/ensembl-genomio"
+      licence:
+        - "Apache License version 2.0"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing meta information
+          e.g. `[ id:'accession1' ]`
+    - fasta_manifest:
+        type: file
+        description: Manifest file listing split FASTA files to recombine.
+        pattern: "*.txt"
+        ontologies: []
+    - agp:
+        type: file
+        description:
+          Optional AGP file describing how split sequence chunks should
+          be recombined. Use NO_FILE when not required.
+        pattern: "*.{agp,NO_FILE}"
+        ontologies: []
+output:
+  recombined_fasta:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing meta information
+            e.g. `[ id:'accession1' ]`
+      - ${meta.id}.fa:
+          type: file
+          description: Recombined FASTA file.
+          pattern: "*.fa"
+          ontologies: []
+  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}:
+          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
+authors:
+  - "ensembl-dev@ebi.ac.uk"
+maintainers:
+  - "ensembl-dev@ebi.ac.uk"
diff --git a/modules/ensembl/fasta/recombine/tests/main.nf.test b/modules/ensembl/fasta/recombine/tests/main.nf.test
new file mode 100644
index 0000000..4448cf7
--- /dev/null
+++ b/modules/ensembl/fasta/recombine/tests/main.nf.test
@@ -0,0 +1,86 @@
+// See the NOTICE file distributed with this work for additional information
+// regarding copyright ownership.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+// nf-core modules test fasta/recombine
+nextflow_process {
+
+    name "Test Process FASTA_RECOMBINE"
+    script "../main.nf"
+    process "FASTA_RECOMBINE"
+
+    tag "modules"
+    tag "modules_ensembl"
+    tag "fasta"
+    tag "fasta/recombine"
+
+    test("stub outputs: header mode") {
+
+        when {
+            options "-stub"
+
+            process {
+                """
+                def manifest = file("manifest.txt")
+                manifest.text = "x\\n"
+
+                def no_file = file("NO_FILE")
+                no_file.text = ""
+
+                input[0] = [
+                    [ id: 'test' ],
+                    manifest,
+                    no_file
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.trace.tasks().size() == 1
+            assert process.out.recombined_fasta.size() == 1
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+    test("stub outputs: AGP mode") {
+
+        when {
+            options "-stub"
+
+            process {
+                """
+                def manifest = file("manifest.txt")
+                manifest.text = "x\\n"
+
+                def agp = file("test.agp")
+                agp.text = ""
+                input[0] = [
+                    [ id: 'test' ],
+                    manifest,
+                    agp
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.trace.tasks().size() == 1
+            assert process.out.recombined_fasta.size() == 1
+            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
new file mode 100644
index 0000000..0357999
--- /dev/null
+++ b/modules/ensembl/fasta/recombine/tests/main.nf.test.snap
@@ -0,0 +1,84 @@
+{
+    "stub outputs: AGP mode": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FASTA_RECOMBINE",
+                        "fasta_recombine",
+                        "1.6.3"
+                    ]
+                ],
+                "recombined_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_fasta_recombine": [
+                    [
+                        "FASTA_RECOMBINE",
+                        "fasta_recombine",
+                        "1.6.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-14T14:39:11.350698",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.3"
+        }
+    },
+    "stub outputs: header mode": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FASTA_RECOMBINE",
+                        "fasta_recombine",
+                        "1.6.3"
+                    ]
+                ],
+                "recombined_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_fasta_recombine": [
+                    [
+                        "FASTA_RECOMBINE",
+                        "fasta_recombine",
+                        "1.6.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-14T14:39:09.216174",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.3"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/ensembl/fasta/split/environment.yml b/modules/ensembl/fasta/split/environment.yml
new file mode 100644
index 0000000..94089f3
--- /dev/null
+++ b/modules/ensembl/fasta/split/environment.yml
@@ -0,0 +1,6 @@
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - ensembl-genomio=1.6.1
diff --git a/modules/ensembl/fasta/split/main.nf b/modules/ensembl/fasta/split/main.nf
new file mode 100644
index 0000000..da643c7
--- /dev/null
+++ b/modules/ensembl/fasta/split/main.nf
@@ -0,0 +1,115 @@
+// See the NOTICE file distributed with this work for additional information
+// regarding copyright ownership.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+process FASTA_SPLIT {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/ensembl-genomio:1.6.1--pyhdfd78af_0'
+        : 'quay.io/biocontainers/ensembl-genomio:1.6.1--pyhdfd78af_0'}"
+
+    input:
+        tuple val(meta), path(fasta), val(longest_seq_bp)
+
+    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
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = []
+
+        if (params.max_seqs_per_file) {
+            args << "--max-seqs-per-file ${params.max_seqs_per_file}"
+        }
+
+        if (params.max_seq_length_per_file) {
+            args << "--max-seq-length-per-file ${params.max_seq_length_per_file}"
+        }
+
+        if (params.min_chunk_length) {
+            args << "--min-chunk-length ${params.min_chunk_length}"
+        }
+
+        if (params.max_files_per_directory) {
+            args << "--max-files-per-directory ${params.max_files_per_directory}"
+        }
+
+        if (params.max_dirs_per_directory) {
+            args << "--max-dirs-per-directory ${params.max_dirs_per_directory}"
+        }
+
+        if (params.force_max_seq_length) {
+            args << "--force-max-seq-length"
+        }
+
+        if (params.write_agp) {
+            args << "--write-agp"
+        }
+
+        if (params.unique_file_names) {
+            args << "--unique-file-names"
+        }
+
+        if (params.delete_existing_files) {
+            args << "--delete-existing-files"
+        }
+
+        """
+        fasta_split \\
+            --fasta-file ${fasta} \\
+            --out-dir splits \\
+            ${args.join(' ')}
+        """
+
+    stub:
+        """
+        layout="default"
+        if [[ "${params.unique_file_names ?: false}" == "true" ]]; then
+            layout="unique"
+        elif [[ -n "${params.max_dirs_per_directory ?: ''}" || -n "${params.max_files_per_directory ?: ''}" ]]; then
+            layout="multi_dir"
+        fi
+
+        mkdir -p splits
+
+        if [[ "\$layout" == "default" ]]; then
+            mkdir -p splits/0
+            touch splits/0/test.1.fa
+            touch splits/0/test.2.fa
+
+        elif [[ "\$layout" == "unique" ]]; then
+            mkdir -p splits/0
+            touch splits/0/test.0.1.fa
+            touch splits/0/test.0.2.fa
+
+        elif [[ "\$layout" == "multi_dir" ]]; then
+            mkdir -p splits/0/0
+            mkdir -p splits/0/1
+            touch splits/0/0/test.1.fa
+            touch splits/0/1/test.2.fa
+        fi
+
+        if [[ "${params.write_agp ?: false}" == "true" ]]; then
+            touch "splits/${meta.id}.agp"
+        fi
+
+        """     
+}
diff --git a/modules/ensembl/fasta/split/meta.yml b/modules/ensembl/fasta/split/meta.yml
new file mode 100644
index 0000000..a00fcba
--- /dev/null
+++ b/modules/ensembl/fasta/split/meta.yml
@@ -0,0 +1,79 @@
+name: "fasta_split"
+description: Split a FASTA file into smaller FASTA files and optionally write an
+  AGP file.
+keywords:
+  - ensembl
+  - fasta
+  - genomics
+  - genomio
+  - split
+tools:
+  - "fasta_split":
+      description: "Split FASTA files with ensembl-genomio."
+      homepage: "https://github.com/Ensembl/ensembl-genomio"
+      licence:
+        - "Apache License version 2.0"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing meta information
+          e.g. `[ id:'accession1' ]`
+    - fasta:
+        type: file
+        description: FASTA file to split.
+        pattern: "*.{fa,fasta,fna}"
+        ontologies: []
+    - longest_seq_bp:
+        type: integer
+        description: Length in base pairs of the longest sequence in the input
+          FASTA.
+output:
+  fastas:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing meta information
+            e.g. `[ id:'accession1' ]`
+      - splits/**/*.fa:
+          type: file
+          description: Split FASTA files.
+          pattern: "splits/**/*.fa"
+          ontologies: []
+  agp:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing meta information
+            e.g. `[ id:'accession1' ]`
+      - splits/*.agp:
+          type: file
+          description: Optional AGP file describing split sequence chunks.
+          pattern: "splits/*.agp"
+          ontologies: []
+  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}:
+          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
+authors:
+  - "ensembl-dev@ebi.ac.uk"
+maintainers:
+  - "ensembl-dev@ebi.ac.uk"
diff --git a/modules/ensembl/fasta/split/tests/main.nf.test b/modules/ensembl/fasta/split/tests/main.nf.test
new file mode 100644
index 0000000..042ff9c
--- /dev/null
+++ b/modules/ensembl/fasta/split/tests/main.nf.test
@@ -0,0 +1,182 @@
+// See the NOTICE file distributed with this work for additional information
+// regarding copyright ownership.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+// nf-core modules test fasta/split
+nextflow_process {
+
+    name "Test Process FASTA_SPLIT"
+    script "../main.nf"
+    process "FASTA_SPLIT"
+
+    tag "modules"
+    tag "modules_ensembl"
+    tag "fasta"
+    tag "fasta/split"
+
+
+    test("stub outputs: default layout, no AGP") {
+
+        when {
+            options "-stub"
+
+            params.write_agp = false
+            params.unique_file_names = false
+            params.max_files_per_directory = null
+            params.max_dirs_per_directory  = null
+
+            process {
+                """
+                input[0] = [[ id:'test' ], file('dummy.fa')]
+                """
+            }
+        }
+
+        then {
+            assert snapshot(process.out).match()
+
+            assert process.out.fastas != null
+            assert process.out.fastas.size() == 1
+
+            def fasta_out = process.out.fastas[0]
+            def meta = fasta_out[0]
+            def fas  = fasta_out[1]
+
+            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
+
+            assertAll(
+                { assert process.success }
+            )
+        }
+    }
+
+    test("stub outputs: AGP optional output appears when enabled") {
+
+        when {
+            options "-stub"
+
+            params.write_agp = true
+            params.unique_file_names = false
+            params.max_files_per_directory = null
+            params.max_dirs_per_directory  = null
+
+            process {
+                """
+                input[0] = [[ id:'test' ], file('dummy.fa')]
+                """
+            }
+        }
+
+        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 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_paths = agp instanceof List ? agp : [agp]
+            def agp_file = path(agp_paths[0]).toFile()
+
+            assert agp_meta.id == "test"
+            assert agp_paths.size() == 1
+            assert agp_file.name == "test.agp"
+
+            assertAll(
+                { assert process.success }
+            )
+        }
+    }
+
+    test("stub outputs: unique_file_names contract") {
+
+        when {
+            options "-stub"
+
+            params.write_agp = false
+            params.unique_file_names = true
+            params.max_files_per_directory = null
+            params.max_dirs_per_directory  = null
+
+            process {
+                """
+                input[0] = [[ id:'test' ], file('dummy.fa')]
+                """
+            }
+        }
+
+        then {
+            assert snapshot(process.out).match()
+
+            def fasta_out = process.out.fastas[0]
+            def fas = fasta_out[1]
+
+            assert fas.size() == 2
+            assert process.out.agp.size() == 0
+
+            // Contract check: names match the unique fixture pattern
+            assert fas.collect { path(it).toFile().name }.sort() == ["test.0.1.fa", "test.0.2.fa"]
+
+            assertAll(
+                { assert process.success }
+            )
+        }
+    }
+
+    test("stub outputs: nested directory layout contract") {
+
+        when {
+            options "-stub"
+
+            params.write_agp = false
+            params.unique_file_names = false
+
+            // Trigger stub's nested fixture selection
+            params.max_files_per_directory = 100
+            params.max_dirs_per_directory  = 100
+
+            process {
+                """
+                input[0] = [[ id:'test' ], file('dummy.fa')]
+                """
+            }
+        }
+
+        then {
+            assert snapshot(process.out).match()
+
+            def fastas = process.out.fastas[0][1]
+            assert fastas.size() == 2
+            assert process.out.agp.size() == 0
+
+            def rels = fastas.collect { path(it).toString() }
+            assert rels.any { it.contains("splits/0/0/") }
+            assert rels.any { it.contains("splits/0/1/") }
+
+            assertAll(
+                { assert process.success }
+            )
+        }
+    }
+}
diff --git a/modules/ensembl/fasta/split/tests/main.nf.test.snap b/modules/ensembl/fasta/split/tests/main.nf.test.snap
new file mode 100644
index 0000000..07ec1d6
--- /dev/null
+++ b/modules/ensembl/fasta/split/tests/main.nf.test.snap
@@ -0,0 +1,224 @@
+{
+    "stub outputs: default layout, no AGP": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.1.fa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.2.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        "FASTA_SPLIT",
+                        "fasta_split",
+                        "1.6.3"
+                    ]
+                ],
+                "agp": [
+                    
+                ],
+                "fastas": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.1.fa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.2.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions_fasta_split": [
+                    [
+                        "FASTA_SPLIT",
+                        "fasta_split",
+                        "1.6.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-14T14:38:41.602246",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.3"
+        }
+    },
+    "stub outputs: AGP optional output appears when enabled": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.1.fa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.2.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.agp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        "FASTA_SPLIT",
+                        "fasta_split",
+                        "1.6.3"
+                    ]
+                ],
+                "agp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.agp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastas": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.1.fa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.2.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions_fasta_split": [
+                    [
+                        "FASTA_SPLIT",
+                        "fasta_split",
+                        "1.6.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-14T14:38:43.765608",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.3"
+        }
+    },
+    "stub outputs: nested directory layout contract": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.1.fa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.2.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        "FASTA_SPLIT",
+                        "fasta_split",
+                        "1.6.3"
+                    ]
+                ],
+                "agp": [
+                    
+                ],
+                "fastas": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.1.fa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.2.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions_fasta_split": [
+                    [
+                        "FASTA_SPLIT",
+                        "fasta_split",
+                        "1.6.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-14T14:38:48.132705",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.3"
+        }
+    },
+    "stub outputs: unique_file_names contract": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.0.1.fa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.0.2.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        "FASTA_SPLIT",
+                        "fasta_split",
+                        "1.6.3"
+                    ]
+                ],
+                "agp": [
+                    
+                ],
+                "fastas": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test.0.1.fa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.0.2.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions_fasta_split": [
+                    [
+                        "FASTA_SPLIT",
+                        "fasta_split",
+                        "1.6.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-14T14:38:45.953655",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.3"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/ensembl/features/combine_json/environment.yml b/modules/ensembl/features/combine_json/environment.yml
new file mode 100644
index 0000000..94089f3
--- /dev/null
+++ b/modules/ensembl/features/combine_json/environment.yml
@@ -0,0 +1,6 @@
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - ensembl-genomio=1.6.1
diff --git a/modules/ensembl/features/combine_json/main.nf b/modules/ensembl/features/combine_json/main.nf
new file mode 100644
index 0000000..e366038
--- /dev/null
+++ b/modules/ensembl/features/combine_json/main.nf
@@ -0,0 +1,126 @@
+// See the NOTICE file distributed with this work for additional information
+// regarding copyright ownership.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+process FEATURES_COMBINE_JSON {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/ensembl-genomio:1.6.1--pyhdfd78af_0'
+        : 'quay.io/biocontainers/ensembl-genomio:1.6.1--pyhdfd78af_0'}"
+
+    input:
+        tuple val(meta), val(analysis), path(json_manifest), path(agp)
+
+    output:
+        tuple val(meta), path("${meta.id}.${analysis}.json"), emit: combined_json
+        tuple val("${task.process}"), val('features_combine_json'), eval("features_combine_json --version"), emit: versions_features_combine_json, topic: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = []
+
+        if (params.chunk_id_regex) {
+            def rx = params.chunk_id_regex.replace("'", "'\"'\"'")
+            args << "--chunk-id-regex '${rx}'"
+        }
+
+        if (params.allow_revcomp) {
+            args << "--allow-revcomp"
+        }
+
+        def has_agp = agp && agp.baseName != 'NO_FILE'
+        if (has_agp) {
+            args << "--agp-file '${agp}'"
+        }
+
+        def out_json = "${meta.id}.${analysis}.json"
+
+        """
+        features_combine_json \\
+            --json-manifest '${json_manifest}' \\
+            --out-json '${out_json}' \\
+            ${args.join(' ')}
+        """
+
+    stub:
+        """
+        out_json="${meta.id}.${analysis}.json"
+
+        test -s "${json_manifest}"
+
+        agp_path="${agp}"
+        agp_name="\${agp_path##*/}"
+
+        manifest_real="\$(python -c 'from pathlib import Path; import sys; print(Path(sys.argv[1]).resolve())' "${json_manifest}")"
+        manifest_dir="\$(dirname "\$manifest_real")"
+
+        first_json="\$(head -n 1 "${json_manifest}")"
+        if [[ -z "\$first_json" ]]; then
+            echo "ERROR: manifest is empty: ${json_manifest}" >&2
+            exit 1
+        fi
+        if [[ "\$first_json" != /* ]]; then
+            first_json="\${manifest_dir}/\${first_json}"
+        fi
+        if [[ ! -s "\$first_json" ]]; then
+            echo "ERROR: first JSON in manifest does not exist or is empty: \$first_json" >&2
+            exit 1
+        fi
+
+        if grep -q '"ncrna_features"' "\$first_json"; then
+            load_type="ncrna"
+        elif grep -q '"repeat_features"' "\$first_json"; then
+            load_type="repeat"
+        else
+            echo "ERROR: cannot detect load type from first JSON: \$first_json" >&2
+            echo "Expected top-level key: 'repeat_features' or 'ncrna_features'." >&2
+            exit 1
+        fi
+
+        if [[ "\$load_type" == "repeat" ]]; then
+            cat > "\$out_json" <<-EOF
+{
+    "analysis": {
+        "logic_name": "stub_repeat"
+    },
+    "source": {
+        "source_provider": "stub"
+    },
+    "repeat_consensus": [],
+    "repeat_features": []
+}
+EOF
+        else
+            cat > "\$out_json" <<-EOF
+{
+    "analysis": {
+        "logic_name": "stub_ncrna"
+    },
+    "source": {
+        "source_provider": "stub"
+    },
+    "ncrna_tool": "stub",
+    "ncrna_features": []
+    }
+EOF
+        fi
+
+        """
+        
+}
diff --git a/modules/ensembl/features/combine_json/meta.yml b/modules/ensembl/features/combine_json/meta.yml
new file mode 100644
index 0000000..049fa1a
--- /dev/null
+++ b/modules/ensembl/features/combine_json/meta.yml
@@ -0,0 +1,75 @@
+name: "features_combine_json"
+description: Combine split feature JSON files into a single JSON file,
+  optionally using an AGP file.
+keywords:
+  - ensembl
+  - features
+  - genomics
+  - genomio
+  - json
+tools:
+  - "features_combine_json":
+      description: "Combine split feature JSON files generated by ensembl-genomio."
+      homepage: "https://github.com/Ensembl/ensembl-genomio"
+      licence:
+        - "Apache License version 2.0"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing meta information
+          e.g. `[ id:'accession1' ]`
+    - analysis:
+        type: string
+        description: Analysis name to include in the combined JSON filename.
+    - json_manifest:
+        type: file
+        description: Manifest file listing split JSON files to combine.
+        pattern: "*.txt"
+        ontologies: []
+    - agp:
+        type: file
+        description:
+          Optional AGP file describing how split sequence chunks should
+          be recombined. Use NO_FILE when not required.
+        pattern: "*.{agp,NO_FILE}"
+        ontologies: []
+output:
+  combined_json:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing meta information
+            e.g. `[ id:'accession1' ]`
+      - ${meta.id}.${analysis}.json:
+          type: file
+          description: Combined feature JSON file.
+          pattern: "*.json"
+          ontologies:
+            - edam: http://edamontology.org/format_3464
+  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}:
+          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
+authors:
+  - "ensembl-dev@ebi.ac.uk"
+maintainers:
+  - "ensembl-dev@ebi.ac.uk"
diff --git a/modules/ensembl/features/combine_json/tests/main.nf.test b/modules/ensembl/features/combine_json/tests/main.nf.test
new file mode 100644
index 0000000..eb6af6d
--- /dev/null
+++ b/modules/ensembl/features/combine_json/tests/main.nf.test
@@ -0,0 +1,163 @@
+// See the NOTICE file distributed with this work for additional information
+// regarding copyright ownership.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+// nf-core modules test features/combine_json
+nextflow_process {
+
+    name "Test Process FEATURES_COMBINE_JSON"
+    script "../main.nf"
+    process "FEATURES_COMBINE_JSON"
+
+    tag "modules"
+    tag "modules_ensembl"
+    tag "features"
+    tag "features/combine_json"
+
+    test("Stub outputs: repeat seq_region mode") {
+
+        when {
+            options "-stub"
+
+            process {
+                """
+                def inJson = file("in.json")
+                inJson.text = '{"repeat_features": []}\\n'
+
+                def manifest = file("manifest.txt")
+                manifest.text = "in.json\\n"
+
+                def noFile = file("NO_FILE")
+                noFile.text = ""
+
+                input[0] = [
+                    [ id:'test' ],
+                    'features',
+                    manifest,
+                    noFile
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.trace.tasks().size() == 1
+            assert process.out.combined_json.size() == 1
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+    test("Stub outputs: ncRNA seq_region mode") {
+
+        when {
+            options "-stub"
+
+            process {
+                """
+                def inJson = file("in.json")
+                inJson.text = '{"ncrna_features": [], "ncrna_tool": "cmscan"}\\n'
+
+                def manifest = file("manifest.txt")
+                manifest.text = "in.json\\n"
+
+                def noFile = file("NO_FILE")
+                noFile.text = ""
+
+                input[0] = [
+                    [ id:'test' ],
+                    'features',
+                    manifest,
+                    noFile
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.trace.tasks().size() == 1
+            assert process.out.combined_json.size() == 1
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+    test("Stub outputs: repeat AGP mode") {
+
+        when {
+            options "-stub"
+
+            process {
+                """
+                def inJson = file("in.json")
+                inJson.text = '{"repeat_features": []}\\n'
+
+                def manifest = file("manifest.txt")
+                manifest.text = "in.json\\n"
+
+                def agp = file("test.agp")
+                agp.text = ""
+
+                input[0] = [
+                    [ id:'test' ],
+                    'features',
+                    manifest,
+                    agp
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.trace.tasks().size() == 1
+            assert process.out.combined_json.size() == 1
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+    test("Stub outputs: ncRNA AGP mode") {
+
+        when {
+            options "-stub"
+
+            process {
+                """
+                def inJson = file("in.json")
+                inJson.text = '{"ncrna_features": [], "ncrna_tool": "cmscan"}\\n'
+
+                def manifest = file("manifest.txt")
+                manifest.text = "in.json\\n"
+
+                def agp = file("test.agp")
+                agp.text = ""
+
+                input[0] = [
+                    [ id:'test' ],
+                    'features',
+                    manifest,
+                    agp
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.trace.tasks().size() == 1
+            assert process.out.combined_json.size() == 1
+            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
new file mode 100644
index 0000000..397c8f0
--- /dev/null
+++ b/modules/ensembl/features/combine_json/tests/main.nf.test.snap
@@ -0,0 +1,166 @@
+{
+    "Stub outputs: repeat AGP mode": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.features.json:md5,aefc84472e26178b64d01051be6d58b2"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FEATURES_COMBINE_JSON",
+                        "features_combine_json",
+                        "1.6.3"
+                    ]
+                ],
+                "combined_json": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.features.json:md5,aefc84472e26178b64d01051be6d58b2"
+                    ]
+                ],
+                "versions_features_combine_json": [
+                    [
+                        "FEATURES_COMBINE_JSON",
+                        "features_combine_json",
+                        "1.6.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-14T14:39:29.784572",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.3"
+        }
+    },
+    "Stub outputs: ncRNA seq_region mode": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.features.json:md5,67c630685f9c819ef28574144c284b4e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FEATURES_COMBINE_JSON",
+                        "features_combine_json",
+                        "1.6.3"
+                    ]
+                ],
+                "combined_json": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.features.json:md5,67c630685f9c819ef28574144c284b4e"
+                    ]
+                ],
+                "versions_features_combine_json": [
+                    [
+                        "FEATURES_COMBINE_JSON",
+                        "features_combine_json",
+                        "1.6.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-14T14:39:27.607529",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.3"
+        }
+    },
+    "Stub outputs: ncRNA AGP mode": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.features.json:md5,67c630685f9c819ef28574144c284b4e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FEATURES_COMBINE_JSON",
+                        "features_combine_json",
+                        "1.6.3"
+                    ]
+                ],
+                "combined_json": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.features.json:md5,67c630685f9c819ef28574144c284b4e"
+                    ]
+                ],
+                "versions_features_combine_json": [
+                    [
+                        "FEATURES_COMBINE_JSON",
+                        "features_combine_json",
+                        "1.6.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-14T14:39:31.963829",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.3"
+        }
+    },
+    "Stub outputs: repeat seq_region mode": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.features.json:md5,aefc84472e26178b64d01051be6d58b2"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FEATURES_COMBINE_JSON",
+                        "features_combine_json",
+                        "1.6.3"
+                    ]
+                ],
+                "combined_json": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.features.json:md5,aefc84472e26178b64d01051be6d58b2"
+                    ]
+                ],
+                "versions_features_combine_json": [
+                    [
+                        "FEATURES_COMBINE_JSON",
+                        "features_combine_json",
+                        "1.6.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-14T14:39:25.403423",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.3"
+        }
+    }
+}
\ No newline at end of file