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add methurator gtestimator and plot modules (#11110)
* add methurator gtestimator and plot modules * add sanitizeOutput and snapshot on summary_report content * add sanitizeOutput and snapshot on summary_report content * update versions output to utilize topics and chanuniform name summary report with methurator_summary * add ontologies, make the description more specific, add topics * add snapshots on the file name and sanitizeOutput * add snapshots on the file name and sanitizeOutput * add topics, lint the process * add topics, update output, update description, add ontologies * update snaps * change the expression in eval to output just version number * add .join().md5 as suggested * update test * Update main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * put all the inputs into one tuple and add ontologies * put inputs into one tuple and minor changes * move args and params to the task.ext.args and make a nextflow.config file for the test * move args into module_args param * add container prefix * add ontologies * remove empty ontologies --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
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‎modules/nf-core/methurator/gtestimator/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::methurator=2.1.1"

‎modules/nf-core/methurator/gtestimator/main.nf‎

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process METHURATOR_GTESTIMATOR {
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tag "${meta.id}"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://depot.galaxyproject.org/singularity/methurator:2.1.1--pyhdfd78af_0'
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: 'quay.io/biocontainers/methurator:2.1.1--pyhdfd78af_0'}"
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input:
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tuple val(meta), path(bam), path(bai), path(fasta)
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output:
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tuple val(meta), path("${prefix}.yml"), emit: summary_report
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tuple val("${task.process}"), val('methurator'), eval("methurator --version | sed 's/.* //'"), emit: versions_methurator, topic: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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methurator gt-estimator \\
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${bam} \\
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--fasta ${fasta} \\
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-@ ${task.cpus} \\
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--outdir . \\
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${args}
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mv methurator_summary.yml ${prefix}.yml
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"""
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stub:
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prefix = task.ext.prefix?: "${meta.id}"
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"""
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touch ${prefix}.yml
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"""
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}

‎modules/nf-core/methurator/gtestimator/meta.yml‎

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name: methurator_gtestimator
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description: |
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Run estimator for DNA methylation sequencing saturation.
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keywords:
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- rrbs
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- BS-seq
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- methylation
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- 5mC
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- methylseq
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- bisulphite
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- bam
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tools:
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- methurator:
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description: |
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Methurator is a Python package designed to estimate CpGs saturation
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for DNA methylation sequencing data.
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homepage: https://github.com/VIBTOBIlab/methurator
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documentation: https://github.com/VIBTOBIlab/methurator/README.md
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licence:
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- "MIT"
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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:'test', single_end:false ]
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- bam:
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type: file
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description: Single BAM file
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pattern: "*.{bam,cram}"
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ontologies:
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- edam: "http://edamontology.org/format_2572" # BAM
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- bai:
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type: file
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description: Single BAM/CRAM index file
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pattern: "*.{bai,crai}"
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ontologies:
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- edam: "http://edamontology.org/format_3327" # BAM index
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- fasta:
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type: file
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description: Input genome fasta file
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pattern: "*.{fasta,fa}"
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ontologies:
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- edam: "http://edamontology.org/format_1332" # FASTA
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output:
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summary_report:
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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:'test', single_end:false ]
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- "${prefix}.yml":
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type: file
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description: |
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YAML file summarizing the saturation analysis results.
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pattern: "${prefix}.yml"
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ontologies:
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- edam: http://edamontology.org/format_3750 # YAML
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versions_methurator:
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- - ${task.process}:
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type: string
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description: methurator gtestimator
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- methurator:
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type: string
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description: The name of the tool
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- methurator --version | sed 's/.* //':
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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: methurator gtestimator
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- methurator:
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type: string
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description: The name of the tool
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- methurator --version | sed 's/.* //':
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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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- "@edogiuili"
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maintainers:
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- "@edogiuili"

‎modules/nf-core/methurator/gtestimator/tests/main.nf.test‎

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nextflow_process {
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name "Test Process METHURATOR_GTESTIMATOR"
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script "../main.nf"
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process "METHURATOR_GTESTIMATOR"
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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 "methurator"
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tag "methurator/gtestimator"
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test("Run methurator gt-estimator on paired-end methylated [bam] | sarscov2 genome [fasta]") {
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when {
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params {
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module_args = '--t-max 10 --minimum-coverage 1 --compute_ci'
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}
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process {
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"""
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input[0] = [ [ id:'test', single_end:false ],
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', 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(
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// Avoid first 3 lines of the summary report as they contain the date and time of the run
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file(process.out.summary_report[0][1]).readLines()[3..10].join('\n').md5(),
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process.out.findAll { key, val -> key.startsWith('versions') }
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).match()}
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)
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}
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}
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test("Run methurator gt-estimator on paired-end methylated [bam] | sarscov2 genome [fasta] - stub") {
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options "-stub"
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when {
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params {
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module_args = '--t-max 10 --minimum-coverage 1 --compute_ci'
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}
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process {
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"""
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input[0] = [ [ id:'test', single_end:false ],
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', 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(sanitizeOutput(process.out)).match() }
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)
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}
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}
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}

‎modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap‎

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{
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"Run methurator gt-estimator on paired-end methylated [bam] | sarscov2 genome [fasta] - stub": {
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"content": [
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{
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"summary_report": [
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[
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{
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"id": "test",
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"single_end": false
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},
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"test.yml:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions_methurator": [
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[
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"METHURATOR_GTESTIMATOR",
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"methurator",
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"2.1.1"
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]
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]
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}
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],
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"timestamp": "2026-04-07T22:41:16.975667",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.10.0"
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}
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},
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"Run methurator gt-estimator on paired-end methylated [bam] | sarscov2 genome [fasta]": {
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"content": [
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"983d27e4d62f86d15a779820758af458",
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{
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"versions_methurator": [
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[
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"METHURATOR_GTESTIMATOR",
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"methurator",
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"2.1.1"
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]
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]
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}
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],
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"timestamp": "2026-04-07T14:33:27.127158",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.10.0"
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}
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}
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}

‎modules/nf-core/methurator/gtestimator/tests/nextflow.config‎

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process {
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withName: METHURATOR_GTESTIMATOR {
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ext.args = params.module_args
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}
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}

‎modules/nf-core/methurator/plot/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::methurator=2.1.1"

‎modules/nf-core/methurator/plot/main.nf‎

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process METHURATOR_PLOT {
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tag "${meta.id}"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://depot.galaxyproject.org/singularity/methurator:2.1.1--pyhdfd78af_0'
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: 'quay.io/biocontainers/methurator:2.1.1--pyhdfd78af_0'}"
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input:
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tuple val(meta), path(summary_report)
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output:
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tuple val(meta), path("plots/*.html"), emit: plots
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tuple val("${task.process}"), val('methurator'), eval("methurator --version | sed 's/.* //'"), emit: versions_methurator, 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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"""
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methurator plot \\
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--summary ${summary_report} \\
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--outdir .
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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mkdir plots/
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touch plots/${prefix}.html
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"""
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}

‎modules/nf-core/methurator/plot/meta.yml‎

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name: methurator_plot
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description: Plots results produced by methurator gtestimator.
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keywords:
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- rrbs
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- BS-seq
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- methylation
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- 5mC
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- methylseq
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- bisulphite
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- bisulfite
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- bam
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tools:
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- methurator:
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description: |
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methurator is a Python package designed to estimate sequencing saturation
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for DNA methylation sequencing data.
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homepage: https://github.com/VIBTOBIlab/methurator
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documentation: https://github.com/VIBTOBIlab/methurator/README.md
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licence:
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- "MIT"
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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:'test', single_end:false ]
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- summary_report:
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type: file
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description: |
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YAML file summarizing the saturation analysis results.
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pattern: "methurator_*.yml"
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ontologies:
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- edam: http://edamontology.org/format_3750 # YAML
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output:
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plots:
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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:'test', single_end:false ]
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- plots/*.html:
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type: file
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description: |
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HTML plots generated from the saturation analysis.
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pattern: "plots/*.html"
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ontologies:
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- edam: "http://edamontology.org/format_2331" # HTML
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versions_methurator:
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- - ${task.process}:
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type: string
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description: methurator plot
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- methurator:
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type: string
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description: The name of the tool
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- methurator --version | sed 's/.* //':
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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: methurator plot
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- methurator:
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type: string
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description: The name of the tool
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- methurator --version | sed 's/.* //':
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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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- "@edogiuili"
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maintainers:
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- "@edogiuili"

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