add cmaple software

modules/nf-core/cmaple/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::cmaple=1.1.0

modules/nf-core/cmaple/main.nf

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+process CMAPLE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/cmaple:1.1.0--h503566f_1':
+        'biocontainers/cmaple:1.1.0--h503566f_1' }"
+
+    input:
+    tuple val(meta), path(aln), path(newick)
+
+    output:
+    tuple val(meta), path("*.treefile"), emit: treefile
+    tuple val(meta), path("*.log")     , emit: log
+    path "versions.yml"                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args     = task.ext.args ?: ''
+    def prefix   = task.ext.prefix ?: "${meta.id}"
+    def tree_arg = newick ? "-t ${newick}" : ""
+    """
+    cmaple-aa \\
+        $args \\
+        -nt $task.cpus \\
+        --prefix ${prefix} \\
+        ${tree_arg} \\
+        -aln $aln
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cmaple: \$(cmaple --help | grep -m1 'CMAPLE version' | sed -E 's/.*version ([0-9.]+).*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo $args
+
+    touch ${prefix}.treefile
+    touch ${prefix}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cmaple: \$(cmaple --help | grep -m1 'CMAPLE version' | sed -E 's/.*version ([0-9.]+).*/\\1/')
+    END_VERSIONS
+    """
+}

modules/nf-core/cmaple/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: cmaple
+description: Efficient phylogenetic tree reconstruction for sequences using the CMAPLE algorithm
+keywords:
+  - phylogeny
+  - phylogenetic tree
+  - maximum likelihood
+  - dna
+  - amino acid
+  - alignment
+  - tree reconstruction
+  - cmaple
+  - iqtree
+tools:
+  - cmaple:
+      description: |
+        CMAPLE (Comprehensive Maximum-likelihood Analysis for Phylogenetic Likelihood Estimation)
+        is an efficient implementation of the MAPLE algorithm for phylogenetic tree reconstruction,
+        particularly optimized for pathogen sequences with low divergence such as SARS-CoV-2.
+        It is integrated within IQ-TREE.
+      homepage: "https://github.com/iqtree/cmaple"
+      documentation: "https://github.com/iqtree/cmaple/wiki/User-Manual"
+      tool_dev_url: "https://github.com/iqtree/cmaple"
+      doi: "10.1093/molbev/msae134"
+      licence: ["GPL-2.0"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - aln:
+        type: file
+        description: Multiple sequence alignment file in FASTA, PHYLIP, or MAPLE format
+        pattern: "*.{fa,fasta,faa,fna,fas,aln,afa,phy,phylip,maple}"
+    - newick:
+        type: file
+        description: A Newick formatted tree based on multiple sequence alignment
+        pattern: "*.{newick,nwk,treefile}"
+        ontologies:
+          - edam: http://edamontology.org/format_1910 # newick
+
+output:
+  treefile:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.treefile":
+          type: file
+          description: Maximum likelihood phylogenetic tree in Newick format
+          pattern: "*.treefile"
+          ontologies:
+            - edam: http://edamontology.org/format_1910 # newick
+  log:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.log":
+          type: file
+          description: Log file containing detailed information about the tree reconstruction process
+          pattern: "*.log"
+          ontologies:
+            - edam: "http://edamontology.org/format_2330" # Textual format
+
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+
+authors:
+  - "@vagkaratzas"
+maintainers:
+  - "@vagkaratzas"

modules/nf-core/cmaple/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process CMAPLE"
+    script "../main.nf"
+    process "CMAPLE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "cmaple"
+    tag "gunzip"
+
+    test("seatoxin - aa - aln") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_aa' ],
+                    file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true),
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log[0][1]).name,
+                    process.out.treefile,
+                    process.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("haemophilus_influenzae - dna - newick - aln") {
+
+        setup {
+            run("GUNZIP") {
+                script "../../gunzip/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id: 'test_gunzip' ],
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz', checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip.map{[
+                    [ id: 'test_dna' ],
+                    it[1],
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk', checkIfExists: true)
+                ]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.log[0][1]).name,
+                    process.out.treefile,
+                    process.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("seatoxin - aa - aln - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_stub' ],
+                    file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true),
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+}

modules/nf-core/cmaple/tests/main.nf.test.snap

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+{
+    "seatoxin - aa - aln - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.treefile:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,975773bfb5d2679d2d0a78e1c5e1444a"
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "treefile": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.treefile:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,975773bfb5d2679d2d0a78e1c5e1444a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-16T13:44:33.656447134"
+    },
+    "haemophilus_influenzae - dna - newick - aln": {
+        "content": [
+            "test_dna.log",
+            [
+                [
+                    {
+                        "id": "test_dna"
+                    },
+                    "test_dna.treefile:md5,bbc5f987e523bda0335ae7a2d70b982c"
+                ]
+            ],
+            [
+                {
+                    "CMAPLE": {
+                        "cmaple": "1.1.0"
+                    }
+                }
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-16T13:44:26.501246515"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,975773bfb5d2679d2d0a78e1c5e1444a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-16T13:44:33.677485714"
+    },
+    "seatoxin - aa - aln": {
+        "content": [
+            "test_aa.log",
+            [
+                [
+                    {
+                        "id": "test_aa"
+                    },
+                    "test_aa.treefile:md5,e8d45477e64ac8aae9ebda4859acdaf1"
+                ]
+            ],
+            [
+                {
+                    "CMAPLE": {
+                        "cmaple": "1.1.0"
+                    }
+                }
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-16T13:44:18.090278163"
+    }
+}