New module: modkit/extract/calls

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

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+process MODKIT_EXTRACT_CALLS {
+    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}" : ''
+    def out_suffix = args.tokenize().contains('--bgzf') ? 'tsv.gz' : 'tsv'
+    """
+    modkit \\
+        extract \\
+        calls \\
+        $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/calls/meta.yml

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+name: modkit_extract_calls
+description: |
+  Produce a per-read per-position table of base modification **calls**
+  (pass/fail/filtered, with the called base) from a modBAM using the same
+  thresholding algorithm as `modkit pileup`. Complementary to `modkit
+  extract full`, which emits raw probabilities: `extract calls` emits the
+  thresholded categorical decision per site per read.
+keywords:
+  - modkit
+  - methylation
+  - extract
+  - calls
+  - 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`).
+        pattern: "*.{bai,csi}"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. `[ id:'mm10' ]`. May be `[[], [], []]` to skip — reference
+          context columns will then be "." in the output.
+    - fasta:
+        type: file
+        description: Optional reference FASTA. Required only to populate reference-context
+          columns in the output.
+        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 call 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/calls/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process MODKIT_EXTRACT_CALLS"
+    script "../main.nf"
+    process "MODKIT_EXTRACT_CALLS"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "modkit"
+    tag "modkit/extract"
+    tag "modkit/extract/calls"
+
+    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/calls/tests/main.nf.test.snap

@@ -0,0 +1,96 @@
+{
+    "homo sapiens - nanopore modbam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,0ce2e5a6bf0889aaf8cbd682e2b17acb"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    [
+                        "MODKIT_EXTRACT_CALLS",
+                        "modkit",
+                        "0.6.1"
+                    ]
+                ],
+                "log": [
+
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,0ce2e5a6bf0889aaf8cbd682e2b17acb"
+                    ]
+                ],
+                "versions_modkit": [
+                    [
+                        "MODKIT_EXTRACT_CALLS",
+                        "modkit",
+                        "0.6.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-23T22:05:37.027585203",
+        "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_CALLS",
+                        "modkit",
+                        "0.6.1"
+                    ]
+                ],
+                "log": [
+
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_modkit": [
+                    [
+                        "MODKIT_EXTRACT_CALLS",
+                        "modkit",
+                        "0.6.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-23T22:05:22.616980777",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.04.6"
+        }
+    }
+}

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

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