New module: modkit/extract/full

modules/nf-core/modkit/extract/full/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/extract/full/main.nf

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+process MODKIT_EXTRACT_FULL {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ont-modkit:0.6.1--hcdda2d0_0':
+        'quay.io/biocontainers/ont-modkit:0.6.1--hcdda2d0_0' }"
+
+    input:
+    tuple val(meta),  path(bam), path(bai)
+    tuple val(meta2), path(fasta), path(fai)
+
+    output:
+    tuple val(meta), path("*.tsv{,.gz}"), emit: tsv
+    tuple val(meta), path("*.log")      , emit: log, optional: true
+    tuple val("${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 reference  = fasta ? "--reference ${fasta}" : ''
+    // BGZF output is detected automatically from --bgzf in ext.args; suffix accordingly
+    def out_suffix = args.tokenize().contains('--bgzf') ? 'tsv.gz' : 'tsv'
+    """
+    modkit \\
+        extract \\
+        full \\
+        $args \\
+        --threads ${task.cpus} \\
+        ${reference} \\
+        ${bam} \\
+        ${prefix}.${out_suffix}
+    """
+
+    stub:
+    def args       = task.ext.args ?: ''
+    def prefix     = task.ext.prefix ?: "${meta.id}"
+    def out_suffix = args.tokenize().contains('--bgzf') ? 'tsv.gz' : 'tsv'
+    """
+    touch ${prefix}.${out_suffix}
+    """
+}

modules/nf-core/modkit/extract/full/meta.yml

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+name: modkit_extract_full
+description: |
+  Transform the probabilities from the MM/ML tags in a modBAM into a
+  tab-separated per-read-per-position table. Emits one row for every
+  modified-base probability call in every read — useful for downstream
+  custom filtering, plotting, and ML training. Optionally BGZF-compressed
+  via `--bgzf` in `ext.args`.
+keywords:
+  - modkit
+  - methylation
+  - extract
+  - read-level
+  - modbam
+  - nanopore
+  - ont
+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 information
+          e.g. `[ id:'sample1' ]`. The output inherits this meta.
+    - bam:
+        type: file
+        description: Input modBAM with MM/ML tags.
+        pattern: "*.{bam,cram}"
+        ontologies:
+          - edam: http://edamontology.org/format_2572
+    - bai:
+        type: file
+        description: BAM index (`.bai` or `.csi`). Optional — if absent, modkit does
+          a serial scan of the BAM (see `--ignore-index`).
+        pattern: "*.{bai,csi}"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. `[ id:'mm10' ]`. May be `[[], [], []]` to skip (modkit works
+          unaligned, but reference context columns will be missing).
+    - fasta:
+        type: file
+        description: Reference FASTA. Required to populate reference-context columns
+          in the output (`ref_kmer`, strand, etc.).
+        pattern: "*.{fa,fasta,fna}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929
+    - fai:
+        type: file
+        description: Samtools FASTA index for `fasta`.
+        pattern: "*.fai"
+        ontologies:
+          - edam: http://edamontology.org/format_3475
+output:
+  tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`.
+      - "*.tsv{,.gz}":
+          type: file
+          description: |
+            Per-read-per-position probability table. BGZF-compressed when
+            `--bgzf` is passed via `ext.args`.
+          pattern: "*.{tsv,tsv.gz}"
+          ontologies:
+            - edam: http://edamontology.org/format_3475
+  log:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`.
+      - "*.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/extract/full/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process MODKIT_EXTRACT_FULL"
+    script "../main.nf"
+    process "MODKIT_EXTRACT_FULL"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "modkit"
+    tag "modkit/extract"
+    tag "modkit/extract/full"
+
+    test("homo sapiens - nanopore modbam - 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)
+                ]
+                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 modbam") {
+
+        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)
+                ]
+                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.tsv },
+                { assert path(process.out.tsv[0][1]).exists() },
+                { assert path(process.out.tsv[0][1]).size() > 0 },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/modkit/extract/full/tests/main.nf.test.snap

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+{
+    "homo sapiens - nanopore modbam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,8300986c98d1b67973439ced4e7f233c"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    [
+                        "MODKIT_EXTRACT_FULL",
+                        "modkit",
+                        "0.6.1"
+                    ]
+                ],
+                "log": [
+
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,8300986c98d1b67973439ced4e7f233c"
+                    ]
+                ],
+                "versions_modkit": [
+                    [
+                        "MODKIT_EXTRACT_FULL",
+                        "modkit",
+                        "0.6.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-23T22:03:49.629847264",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.04.6"
+        }
+    },
+    "homo sapiens - nanopore modbam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    [
+                        "MODKIT_EXTRACT_FULL",
+                        "modkit",
+                        "0.6.1"
+                    ]
+                ],
+                "log": [
+
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_modkit": [
+                    [
+                        "MODKIT_EXTRACT_FULL",
+                        "modkit",
+                        "0.6.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-23T22:03:35.292337916",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.04.6"
+        }
+    }
+}

modules/nf-core/modkit/extract/full/tests/nextflow.config

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