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feat: add modkit/extract/calls module
Add new nf-core module wrapping `modkit extract calls`, which emits a per-read per-position table of base modification calls using the same pass/fail thresholding as `modkit pileup`. Complementary to `modkit/extract/full` (raw probabilities): this module emits the thresholded categorical decisions. Useful for per-read downstream analysis such as allele-specific methylation and methylation-aware phasing. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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‎modules/nf-core/modkit/extract/calls/environment.yml‎

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

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

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process MODKIT_EXTRACT_CALLS {
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tag "$meta.id"
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label 'process_high'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ont-modkit:0.6.1--hcdda2d0_0':
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'quay.io/biocontainers/ont-modkit:0.6.1--hcdda2d0_0' }"
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input:
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tuple val(meta), path(bam), path(bai)
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tuple val(meta2), path(fasta), path(fai)
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output:
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tuple val(meta), path("*.tsv{,.gz}"), emit: tsv
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tuple val(meta), path("*.log") , emit: log, optional: true
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tuple val("${task.process}"), val('modkit'), eval("modkit --version | sed 's/modkit //'"), emit: versions_modkit, topic: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def reference = fasta ? "--reference ${fasta}" : ''
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def out_suffix = args.tokenize().contains('--bgzf') ? 'tsv.gz' : 'tsv'
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"""
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modkit \\
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extract \\
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calls \\
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$args \\
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--threads ${task.cpus} \\
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${reference} \\
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${bam} \\
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${prefix}.${out_suffix}
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"""
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stub:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def out_suffix = args.tokenize().contains('--bgzf') ? 'tsv.gz' : 'tsv'
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"""
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touch ${prefix}.${out_suffix}
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"""
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}

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

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name: modkit_extract_calls
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description: |
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Produce a per-read per-position table of base modification **calls**
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(pass/fail/filtered, with the called base) from a modBAM using the same
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thresholding algorithm as `modkit pileup`. Complementary to `modkit
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extract full`, which emits raw probabilities: `extract calls` emits the
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thresholded categorical decision per site per read.
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keywords:
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- modkit
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- methylation
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- extract
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- calls
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- read-level
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- modbam
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- nanopore
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- ont
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tools:
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- "modkit":
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description: A bioinformatics tool for working with modified bases in Oxford Nanopore
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sequencing data.
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homepage: https://github.com/nanoporetech/modkit
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documentation: https://nanoporetech.github.io/modkit/
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tool_dev_url: https://github.com/nanoporetech/modkit
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licence:
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- "Oxford Nanopore Technologies PLC. Public License Version 1.0"
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identifier: ""
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`. The output inherits this meta.
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- bam:
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type: file
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description: Input modBAM with MM/ML tags.
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pattern: "*.{bam,cram}"
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ontologies:
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- edam: http://edamontology.org/format_2572
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- bai:
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type: file
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description: BAM index (`.bai` or `.csi`).
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pattern: "*.{bai,csi}"
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ontologies: []
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- - meta2:
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type: map
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description: |
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Groovy Map containing reference information
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e.g. `[ id:'mm10' ]`. May be `[[], [], []]` to skip — reference
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context columns will then be "." in the output.
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- fasta:
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type: file
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description: Optional reference FASTA. Required only to populate reference-context
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columns in the output.
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pattern: "*.{fa,fasta,fna}"
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ontologies:
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- edam: http://edamontology.org/format_1929
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- fai:
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type: file
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description: Samtools FASTA index for `fasta`.
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pattern: "*.fai"
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ontologies:
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- edam: http://edamontology.org/format_3475
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output:
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tsv:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`.
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- "*.tsv{,.gz}":
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type: file
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description: |
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Per-read per-position call table. BGZF-compressed when `--bgzf`
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is passed via `ext.args`.
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pattern: "*.{tsv,tsv.gz}"
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ontologies:
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- edam: http://edamontology.org/format_3475
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log:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`.
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- "*.log":
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type: file
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description: |
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Optional modkit debug log (only emitted when `--log-filepath
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<name>.log` is passed via `ext.args`).
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pattern: "*.log"
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ontologies: []
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versions_modkit:
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- - ${task.process}:
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type: string
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description: The name of the process
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- modkit:
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type: string
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description: The name of the tool
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- modkit --version | sed 's/modkit //':
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type: eval
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description: The expression to obtain the version of the tool
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topics:
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versions:
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- - ${task.process}:
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type: string
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description: The name of the process
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- modkit:
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type: string
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description: The name of the tool
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- modkit --version | sed 's/modkit //':
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type: eval
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description: The expression to obtain the version of the tool
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authors:
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- "@sahuno"
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maintainers:
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- "@sahuno"

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

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nextflow_process {
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name "Test Process MODKIT_EXTRACT_CALLS"
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script "../main.nf"
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process "MODKIT_EXTRACT_CALLS"
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config "./nextflow.config"
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tag "modules"
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tag "modules_nfcore"
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tag "modkit"
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tag "modkit/extract"
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tag "modkit/extract/calls"
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test("homo sapiens - nanopore modbam - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [
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[ id: 'test' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true)
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]
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input[1] = [
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[ id: 'genome' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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test("homo sapiens - nanopore modbam") {
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when {
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process {
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"""
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input[0] = [
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[ id: 'test' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true)
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]
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input[1] = [
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[ id: 'genome' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert process.out.tsv },
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{ assert path(process.out.tsv[0][1]).exists() },
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{ assert path(process.out.tsv[0][1]).size() > 0 },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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}

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

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

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

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process {
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withName: 'MODKIT_EXTRACT_CALLS' {
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ext.args = ''
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}
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}

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