feat: add dorado/aligner module

.github/skip_nf_test.json

@@ -46,6 +46,7 @@
         "modules/nf-core/deepvariant/vcfstatsreport",
         "subworkflows/nf-core/dia_proteomics_analysis",
         "modules/nf-core/diann",
+        "modules/nf-core/dorado",
         "modules/nf-core/doubletdetection",
         "modules/nf-core/fastk/fastk",
         "modules/nf-core/fastk/histex",

.nf-core.yml

@@ -6,6 +6,7 @@ container-registry:
   - ghcr.io/nbisweden
   - ghcr.io/scverse
   - nvcr.io/nvidia/clara
+  - docker.io/nanoporetech
   - docker.io/biocontainers
   - docker.io/labsyspharm
   - docker.io/google

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

@@ -0,0 +1,5 @@
+---
+# 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

@@ -0,0 +1,50 @@
+process DORADO_ALIGNER {
+    tag "$meta.id"
+    label 'process_high'
+
+    // dorado is not on bioconda (ONTPL licence). Using
+    // Docker Hub image directly. SHA tag pins to v1.4.0; a semver tag is tracked in
+    // nanoporetech/dorado#1584. Same pattern as nf-core/parabricks modules.
+    conda null
+    container "docker.io/nanoporetech/dorado:shac8f356489fa8b44b31beba841b84d2879de2088e"
+
+    input:
+    tuple val(meta), path(bam)                          // unaligned BAM produced by dorado basecaller
+    tuple val(meta2), path(reference), path(fai)        // reference FASTA (or .mmi index) and .fai
+
+    output:
+    tuple val(meta), path("*.bam")                   , emit: bam
+    tuple val(meta), path("*.sequencing_summary.txt"), emit: summary, optional: true
+    tuple val("${task.process}"), val('dorado'), eval("dorado --version 2>&1 | head -1"), 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
+
+    # --emit-summary writes a fixed-name `sequencing_summary.txt` into the work
+    # directory; prefix it so outputs stay per-sample.
+    if [ -f sequencing_summary.txt ]; then
+        mv sequencing_summary.txt ${prefix}.sequencing_summary.txt
+    fi
+    """
+
+    stub:
+    def args    = task.ext.args ?: ''
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def summary = args.contains('--emit-summary') ? "touch ${prefix}.sequencing_summary.txt" : ''
+    """
+    touch ${prefix}.bam
+    ${summary}
+    """
+}

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

@@ -0,0 +1,116 @@
+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: |
+          BAM file to align, typically the unaligned output of dorado
+          basecaller. Any HTS-format input is accepted; an already-aligned BAM is
+          realigned. Modified base tags (MM/ML) and other BAM auxiliary 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 ]`
+      - "*.sequencing_summary.txt":
+          type: file
+          description: |
+            Per-read alignment summary, present only when `--emit-summary` is set
+            in `ext.args`. dorado writes this as a fixed-name
+            `sequencing_summary.txt`; the module renames it to
+            `<prefix>.sequencing_summary.txt` so outputs stay per-sample.
+          pattern: "*.sequencing_summary.txt"
+          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:
+          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:
+          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

@@ -0,0 +1,89 @@
+nextflow_process {
+
+    name "Test Process DORADO_ALIGNER"
+    script "../main.nf"
+    process "DORADO_ALIGNER"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "dorado"
+    tag "dorado/aligner"
+
+    test("homo sapiens - nanopore bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.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() }
+            )
+        }
+    }
+
+    test("homo sapiens - nanopore bam") {
+
+        // dorado aligner accepts any HTS input; the reads in this fixture are
+        // realigned against the chr22 subset reference.
+        //
+        // Neither a whole-file md5 nor nft-bam's readsMD5 is usable here: the BAM
+        // header carries environment-dependent values (@PG CL: paths, @SQ UR:), and
+        // dorado writes records in a thread-dependent order with SO:unknown, so the
+        // reads md5 differs between runs on the same input. The record count is
+        // snapshotted instead, with the alignment itself checked by assertion.
+        //
+        // test2.sorted.bam is used rather than test.sorted.phased.bam because the
+        // latter's records each carry two RG tags (one from minimap2 -R, one from
+        // the original dorado basecall) while its header declares only one. dorado
+        // preserves both, so the output trips htsjdk's READ_GROUP_NOT_FOUND check.
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test2.sorted.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 process.out.bam },
+                // --emit-summary is set in nextflow.config, so the optional
+                // summary channel must be populated and correctly prefixed
+                { assert process.out.summary },
+                { assert file(process.out.summary[0][1]).name == 'test.sequencing_summary.txt' },
+                { assert path(process.out.summary[0][1]).readLines().size() > 1 },
+                { assert snapshot([
+                    bam_name : file(process.out.bam[0][1]).name,
+                    n_records: bam(process.out.bam[0][1]).getReads().size(),
+                    versions : process.out.versions_dorado
+                ]).match() }
+            )
+        }
+    }
+}

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

@@ -0,0 +1,79 @@
+{
+    "homo sapiens - nanopore bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.sequencing_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        "DORADO_ALIGNER",
+                        "dorado",
+                        "1.4.0+ba44a013"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.sequencing_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_dorado": [
+                    [
+                        "DORADO_ALIGNER",
+                        "dorado",
+                        "1.4.0+ba44a013"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-09-06T13:17:37.534043326",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo sapiens - nanopore bam": {
+        "content": [
+            {
+                "bam_name": "test.bam",
+                "n_records": 159,
+                "versions": [
+                    [
+                        "DORADO_ALIGNER",
+                        "dorado",
+                        "1.4.0+ba44a013"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-09-06T13:17:49.195776876",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}

modules/nf-core/dorado/aligner/tests/nextflow.config

@@ -0,0 +1,6 @@
+process {
+    withName: 'DORADO_ALIGNER' {
+        // exercise the optional per-read summary output
+        ext.args = '--emit-summary'
+    }
+}