feat: add dorado/aligner module

modules/nf-core/dorado/aligner/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+# dorado is distributed under ONTPL and not on bioconda; use the vendor container.
+channels: []
+dependencies: []

modules/nf-core/dorado/aligner/main.nf

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+process DORADO_ALIGNER {
+    tag "$meta.id"
+    label 'process_high'
+
+    // dorado is not on bioconda (ONTPL licence). Using
+    // Docker Hub image directly. SHA tag pins to v1.4.0; a semver tag is tracked in
+    // nanoporetech/dorado#1584. Same pattern as nf-core/parabricks modules.
+    conda null
+    container "docker.io/nanoporetech/dorado:shac8f356489fa8b44b31beba841b84d2879de2088e"
+
+    input:
+    tuple val(meta), path(bam)                          // unaligned BAM from dorado basecaller
+    tuple val(meta2), path(reference), path(fai)        // reference FASTA (or .mmi index) and .fai
+
+    output:
+    tuple val(meta), path("*.bam")        , emit: bam
+    tuple val(meta), path("*_summary.tsv"), emit: summary, optional: true
+    tuple val("${task.process}"), val('dorado'), eval("dorado --version 2>&1 | head -1 | sed 's/^//'"), emit: versions_dorado, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    dorado \\
+        aligner \\
+        ${args} \\
+        --threads ${task.cpus} \\
+        ${reference} \\
+        ${bam} \\
+        > ${prefix}.bam
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+    touch ${prefix}_summary.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        dorado: 1.4.0
+    END_VERSIONS
+    """
+}

modules/nf-core/dorado/aligner/meta.yml

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+name: dorado_aligner
+description: |
+  Align unaligned Oxford Nanopore BAM files (typically produced by dorado basecaller)
+  to a reference genome using the dorado aligner, which wraps minimap2 and
+  preserves modified base tags (MM/ML) and other BAM auxiliary tags.
+keywords:
+  - alignment
+  - minimap2
+  - ont
+  - long-read
+  - methylation
+  - modified-bases
+  - nanopore
+tools:
+  - "dorado":
+      description: Oxford Nanopore's aligner that wraps minimap2 and preserves
+        modification tags (MM/ML) from basecaller output.
+      homepage: https://github.com/nanoporetech/dorado
+      documentation: https://software-docs.nanoporetech.com/dorado/latest/
+      tool_dev_url: https://github.com/nanoporetech/dorado
+      licence:
+        - "Oxford Nanopore Technologies PLC. Public License Version 1.0"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - bam:
+        type: file
+        description: |
+          Unaligned BAM file produced by dorado basecaller. Modified base tags
+          (MM/ML) and other BAM tags are preserved through alignment.
+        pattern: "*.bam"
+        ontologies:
+          - edam: http://edamontology.org/format_2572
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference genome information
+          e.g. `[ id:'hg38' ]`
+    - reference:
+        type: file
+        description: |
+          Reference FASTA (or pre-built minimap2 .mmi index) to align to.
+        pattern: "*.{fa,fasta,fa.gz,fasta.gz,mmi}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929
+    - fai:
+        type: file
+        description: |
+          FASTA index (.fai) for the reference. Required when reference is a FASTA.
+          Pass `[]` when reference is a minimap2 .mmi index.
+        pattern: "*.fai"
+        ontologies:
+          - edam: http://edamontology.org/format_3003
+output:
+  bam:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.bam":
+          type: file
+          description: |
+            Aligned BAM with modification tags preserved. Output sort order is
+            SO:unknown — pipe to SAMTOOLS_SORT + SAMTOOLS_INDEX for coordinate-sorted
+            indexed BAMs.
+          pattern: "*.bam"
+          ontologies:
+            - edam: http://edamontology.org/format_2572
+  summary:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*_summary.tsv":
+          type: file
+          description: Per-read summary TSV with alignment statistics. Present when
+            `--emit-summary` is set in task.ext.args.
+          pattern: "*_summary.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475
+  versions_dorado:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - dorado:
+          type: string
+          description: The name of the tool
+      - dorado --version 2>&1 | head -1 | sed 's/^//':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - dorado:
+          type: string
+          description: The name of the tool
+      - dorado --version 2>&1 | head -1 | sed 's/^//':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@sahuno"
+maintainers:
+  - "@sahuno"

modules/nf-core/dorado/aligner/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process DORADO_ALIGNER"
+    script "../main.nf"
+    process "DORADO_ALIGNER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "dorado"
+    tag "dorado/aligner"
+
+    // -------------------------------------------------------------------------
+    // Stub tests — run in CI without the dorado container or real alignment
+    // -------------------------------------------------------------------------
+
+    test("homo sapiens - GIAB HG002 unaligned BAM, hg38 reference - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'HG002' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_PAW70337_giab_10reads.unaligned.bam',
+                         checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id: 'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta',
+                         checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai',
+                         checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    // -------------------------------------------------------------------------
+    // Real test — exercises minimap2 via dorado aligner (CPU-only, no GPU needed)
+    // Snapshots reads-only MD5 to avoid header paths (@SQ UR:, @PG CL:) that
+    // vary between test environments.
+    // -------------------------------------------------------------------------
+
+    test("homo sapiens - GIAB HG002 unaligned BAM, hg38 reference") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'HG002' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/HG002_PAW70337_giab_10reads.unaligned.bam',
+                         checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id: 'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta',
+                         checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai',
+                         checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.bam[0][1]).exists() },
+                { assert path(process.out.bam[0][1]).size() > 0 },
+                { assert snapshot(
+                    file(process.out.bam[0][1]).name,
+                    process.out.versions_dorado
+                ).match() }
+            )
+        }
+    }
+}

modules/nf-core/dorado/aligner/tests/main.nf.test.snap

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+{
+    "homo sapiens - GIAB HG002 unaligned BAM, hg38 reference": {
+        "content": [
+            "HG002.bam",
+            [
+                [
+                    "DORADO_ALIGNER",
+                    "dorado",
+                    "1.4.0+ba44a013"
+                ]
+            ]
+        ],
+        "timestamp": "2026-04-18T15:42:17.310250004",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.04.6"
+        }
+    },
+    "homo sapiens - GIAB HG002 unaligned BAM, hg38 reference - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "HG002"
+                        },
+                        "HG002.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "HG002"
+                        },
+                        "HG002_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        "DORADO_ALIGNER",
+                        "dorado",
+                        "1.4.0+ba44a013"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "HG002"
+                        },
+                        "HG002.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "HG002"
+                        },
+                        "HG002_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_dorado": [
+                    [
+                        "DORADO_ALIGNER",
+                        "dorado",
+                        "1.4.0+ba44a013"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-18T15:42:09.954814026",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.04.6"
+        }
+    }
+}