New module: modkit/validate

modules/nf-core/modkit/validate/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::ont-modkit=0.6.1"

modules/nf-core/modkit/validate/main.nf

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+process MODKIT_VALIDATE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ont-modkit:0.6.1--hcdda2d0_0':
+        'quay.io/biocontainers/ont-modkit:0.6.1--hcdda2d0_0' }"
+
+    input:
+    // Multiple sample pairs can be supplied as list inputs; BAMs and BEDs are
+    // paired by index and passed as repeated `--bam-and-bed <BAM> <BED>`.
+    tuple val(meta),  path(bams, stageAs: "bams/?/*"), path(bais, stageAs: "bais/?/*"), path(truth_beds, stageAs: "truth/?/*")
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    tuple val(meta), path("*.log"), emit: log, optional: true
+    tuple val("${task.process}"), val('modkit'), eval("modkit --version | sed 's/modkit //'"), emit: versions_modkit, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args       = task.ext.args ?: ''
+    def prefix     = task.ext.prefix ?: "${meta.id}"
+    def bam_list   = bams       instanceof List ? bams       : [bams]
+    def bed_list   = truth_beds instanceof List ? truth_beds : [truth_beds]
+    if (bam_list.size() != bed_list.size()) {
+        error "MODKIT_VALIDATE: bams and truth_beds must have the same length (got ${bam_list.size()} vs ${bed_list.size()})"
+    }
+    def pair_args  = [bam_list, bed_list].transpose().collect { b, g -> "--bam-and-bed ${b} ${g}" }.join(' ')
+    """
+    modkit \\
+        validate \\
+        $args \\
+        --threads ${task.cpus} \\
+        ${pair_args} \\
+        --out-filepath ${prefix}.tsv
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tsv
+    """
+}

modules/nf-core/modkit/validate/meta.yml

@@ -0,0 +1,110 @@
+name: modkit_validate
+description: |
+  Validate base modification calls in one or more mod-BAMs against a matched
+  ground-truth BED file containing the expected modification state at
+  reference positions. Reports per-sample and combined confusion-matrix style
+  statistics (accuracy, filtered calls, probability distribution) as a
+  tab-separated machine-parseable table.
+keywords:
+  - modkit
+  - methylation
+  - validate
+  - nanopore
+  - ont
+  - modbam
+  - ground-truth
+  - benchmark
+tools:
+  - "modkit":
+      description: A bioinformatics tool for working with modified bases in Oxford Nanopore
+        sequencing data.
+      homepage: https://github.com/nanoporetech/modkit
+      documentation: https://nanoporetech.github.io/modkit/
+      tool_dev_url: https://github.com/nanoporetech/modkit
+      licence:
+        - "Oxford Nanopore Technologies PLC. Public License Version 1.0"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample (or cohort) information
+          e.g. `[ id:'test_run' ]`. The output inherits this meta.
+    - bams:
+        type: list
+        description: |
+          One or more modBAM files. BAMs are paired 1:1 with `truth_beds`
+          by list index and passed as repeated `--bam-and-bed <BAM> <BED>`
+          arguments to `modkit validate`.
+        pattern: "*.{bam,cram}"
+        ontologies:
+          - edam: http://edamontology.org/format_2572
+    - bais:
+        type: list
+        description: |
+          BAM indices (`.bai` or `.csi`) matching each input BAM.
+        pattern: "*.{bai,csi}"
+        ontologies: []
+    - truth_beds:
+        type: list
+        description: |
+          Ground-truth BED files (one per BAM). The name field must be the
+          short modified base code (single letter or ChEBI ID) or `-` to
+          mark a canonical reference position. Paired 1:1 with `bams`.
+        pattern: "*.{bed,bed.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_3003
+output:
+  tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test_run' ]`.
+      - "*.tsv":
+          type: file
+          description: |
+            Machine-parseable validation summary produced by
+            `modkit validate --out-filepath`. Columns include counts of
+            correct / incorrect / filtered calls per class.
+          pattern: "*.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475
+  log:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test_run' ]`.
+      - "*.log":
+          type: file
+          description: |
+            Optional modkit debug log (only emitted when `--log-filepath
+            <name>.log` is passed via `ext.args`).
+          pattern: "*.log"
+          ontologies: []
+  versions_modkit:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - modkit:
+          type: string
+          description: The name of the tool
+      - modkit --version | sed 's/modkit //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - modkit:
+          type: string
+          description: The name of the tool
+      - modkit --version | sed 's/modkit //':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@sahuno"
+maintainers:
+  - "@sahuno"

modules/nf-core/modkit/validate/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process MODKIT_VALIDATE"
+    script "../main.nf"
+    process "MODKIT_VALIDATE"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "modkit"
+    tag "modkit/validate"
+    tag "modkit/pileup"
+
+    // A real validation run needs a BAM paired with a ground-truth BED whose
+    // `name` column is the short modified-base code (m/h/a/...) or `-` for a
+    // canonical reference position.
+    //
+    // The public modules test data doesn't ship such a BED, so for the real
+    // test we pipe `MODKIT_PILEUP` output through `cut -f1-6` (a bedMethyl's
+    // first six columns already satisfy the BED6 + mod-code-in-name contract)
+    // and validate the BAM against its own pileup. This is a self-consistency
+    // smoke test — it won't produce meaningful accuracy metrics but will
+    // exercise the full CLI path end-to-end.
+    setup {
+        run("MODKIT_PILEUP") {
+            script "../../pileup/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [[],[],[]]
+                input[2] = [[],[]]
+                """
+            }
+        }
+    }
+
+    test("homo sapiens - modbam + truth bed - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true) ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true) ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ]  // placeholder truth BED for stub — real validation needs a truth BED whose name column is the mod code (m/h/-)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/modkit/validate/tests/main.nf.test.snap

@@ -0,0 +1,49 @@
+{
+    "homo sapiens - modbam + truth bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    [
+                        "MODKIT_VALIDATE",
+                        "modkit",
+                        "0.6.1"
+                    ]
+                ],
+                "log": [
+
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_modkit": [
+                    [
+                        "MODKIT_VALIDATE",
+                        "modkit",
+                        "0.6.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-23T22:01:55.666359485",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.04.6"
+        }
+    }
+}

modules/nf-core/modkit/validate/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: 'MODKIT_VALIDATE' {
+        ext.args = '-c C'
+    }
+}