add methurator gtestimator and plot modules

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

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

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

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

@@ -0,0 +1,82 @@
+name: methurator_gtestimator
+description: |
+  Run estimator for DNA methylation sequencing saturation.
+keywords:
+  - rrbs
+  - BS-seq
+  - methylation
+  - 5mC
+  - methylseq
+  - bisulphite
+  - bam
+tools:
+  - methurator:
+      description: |
+        Methurator is a Python package designed to estimate CpGs saturation
+        for DNA methylation sequencing data.
+      homepage: https://github.com/VIBTOBIlab/methurator
+      documentation: https://github.com/VIBTOBIlab/methurator/README.md
+      licence:
+        - "MIT"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+        ontologies: []
+    - bam:
+        type: file
+        description: Single BAM file
+        pattern: "*.{bam,cram}"
+        ontologies: []
+    - bai:
+        type: file
+        description: Single BAM/CRAM index file
+        pattern: "*.{bai,crai}"
+        ontologies: []
+    - fasta:
+        type: file
+        description: Input genome fasta file
+        pattern: "*.{fasta,fa}"
+        ontologies: []
+output:
+  summary_report:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          ontologies: []
+      - "${prefix}.yml":
+          type: file
+          description: |
+            YAML file summarizing the saturation analysis results.
+          pattern: "${prefix}.yml"
+          ontologies: []
+  versions_methurator:
+    - - ${task.process}:
+          type: string
+          description: methurator gtestimator
+      - methurator:
+          type: string
+          description: The name of the tool
+      - methurator --version | sed 's/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: methurator gtestimator
+      - methurator:
+          type: string
+          description: The name of the tool
+      - methurator --version | sed 's/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@edogiuili"
+maintainers:
+  - "@edogiuili"

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

@@ -0,0 +1,68 @@
+nextflow_process {
+
+    name "Test Process METHURATOR_GTESTIMATOR"
+    script "../main.nf"
+    process "METHURATOR_GTESTIMATOR"
+    config './nextflow.config'
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "methurator"
+    tag "methurator/gtestimator"
+
+    test("Run methurator gt-estimator on paired-end methylated [bam] | sarscov2 genome [fasta]") {
+
+        when {
+            params {
+                module_args = '--t-max 10 --minimum-coverage 1 --compute_ci'
+            }
+
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    // Avoid first 3 lines of the summary report as they contain the date and time of the run
+                    file(process.out.summary_report[0][1]).readLines()[3..10].join('\n').md5(),
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match()}
+            )
+        }
+    }
+    test("Run methurator gt-estimator on paired-end methylated [bam] | sarscov2 genome [fasta] - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                module_args = '--t-max 10 --minimum-coverage 1 --compute_ci'
+            }
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+}

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

@@ -0,0 +1,48 @@
+{
+    "Run methurator gt-estimator on paired-end methylated [bam] | sarscov2 genome [fasta] - stub": {
+        "content": [
+            {
+                "summary_report": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.yml:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_methurator": [
+                    [
+                        "METHURATOR_GTESTIMATOR",
+                        "methurator",
+                        "2.1.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-07T22:41:16.975667",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.0"
+        }
+    },
+    "Run methurator gt-estimator on paired-end methylated [bam] | sarscov2 genome [fasta]": {
+        "content": [
+            "983d27e4d62f86d15a779820758af458",
+            {
+                "versions_methurator": [
+                    [
+                        "METHURATOR_GTESTIMATOR",
+                        "methurator",
+                        "2.1.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-07T14:33:27.127158",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.0"
+        }
+    }
+}

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

@@ -0,0 +1,5 @@
+process {
+    withName: METHURATOR_GTESTIMATOR {
+        ext.args = params.module_args
+    }
+}

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

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

@@ -0,0 +1,35 @@
+process METHURATOR_PLOT {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/methurator:2.1.1--pyhdfd78af_0'
+        : 'biocontainers/methurator:2.1.1--pyhdfd78af_0'}"
+
+    input:
+    tuple val(meta), path(summary_report)
+
+    output:
+    tuple val(meta), path("plots/*.html"), emit: plots
+    tuple val("${task.process}"), val('methurator'), eval("methurator --version | sed 's/.* //'"), emit: versions_methurator, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+    methurator plot \\
+        --summary ${summary_report} \\
+        --outdir .
+
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir plots/
+    touch plots/${prefix}.html
+
+    """
+}

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

@@ -0,0 +1,74 @@
+name: methurator_plot
+description: Plots results produced by methurator gtestimator.
+keywords:
+  - rrbs
+  - BS-seq
+  - methylation
+  - 5mC
+  - methylseq
+  - bisulphite
+  - bisulfite
+  - bam
+tools:
+  - methurator:
+      description: |
+        methurator is a Python package designed to estimate sequencing saturation
+        for DNA methylation sequencing data.
+      homepage: https://github.com/VIBTOBIlab/methurator
+      documentation: https://github.com/VIBTOBIlab/methurator/README.md
+      licence:
+        - "MIT"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+        ontologies: []
+    - summary_report:
+        type: file
+        description: |
+          YAML file summarizing the saturation analysis results.
+        pattern: "methurator_*.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+output:
+  plots:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          ontologies: []
+      - plots/*.html:
+          type: file
+          description: |
+            HTML plots generated from the saturation analysis.
+          pattern: "plots/*.html"
+          ontologies: []
+  versions_methurator:
+    - - ${task.process}:
+          type: string
+          description: methurator plot
+      - methurator:
+          type: string
+          description: The name of the tool
+      - methurator --version | sed 's/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: methurator plot
+      - methurator:
+          type: string
+          description: The name of the tool
+      - methurator --version | sed 's/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@edogiuili"
+maintainers:
+  - "@edogiuili"