ENSGENOMIO-18 Chunking modules

.gitignore

@@ -1,2 +1,5 @@
 .nextflow*
 .nf-test*
+__pycache__/
+*.pyc
+.python-version

modules/ensembl/fasta/recombine/environment.yml

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+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - ensembl-genomio=1.6.1

modules/ensembl/fasta/recombine/main.nf

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+// 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"
+        """   
+}

modules/ensembl/fasta/recombine/meta.yml

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+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"

modules/ensembl/fasta/recombine/tests/main.nf.test

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+// 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()
+        }
+    }
+}

modules/ensembl/fasta/recombine/tests/main.nf.test.snap

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+{
+    "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"
+        }
+    }
+}

modules/ensembl/fasta/split/environment.yml

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+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - ensembl-genomio=1.6.1