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

@@ -0,0 +1,52 @@
+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)
+    tuple val(meta2), path(bai)
+    tuple val(meta3), path(fasta)
+
+    output:
+    tuple val(meta), path("methurator_*.yml")    , emit: summary_report
+    path  "versions.yml"                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    if(params.rrbs) { args += '--rrbs'}
+    """
+    methurator gt-estimator \\
+        $bam \\
+        --fasta $fasta \\
+        --minimum-coverage ${params.minimum_coverage} \\
+        --t-max ${params.t_max} \\
+        -@ ${task.cpus} \\
+        --outdir . \\
+        --compute_ci \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        methurator: "\$(methurator --version 2>&1 | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/')"
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "methurator_summary_${meta.id}"
+    """
+    touch ${prefix}.yml
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        methurator: "\$(methurator --version 2>&1 | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/')"
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,71 @@
+name: methurator_gtestimator
+description: |
+  Methurator is a Python package designed to estimate CpGs saturation
+  for DNA methylation sequencing data.
+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 ]
+    - bam:
+        type: file
+        description: BAM/CRAM file
+        pattern: "*.{bam,cram}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bai:
+        type: file
+        description: BAM/CRAM index file
+        pattern: "*.{bai,crai}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+        pattern: "*.{fasta,fa}"
+output:
+  summary_report:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "methurator_*.yml":
+          type: file
+          description: |
+            YAML file summarizing the saturation analysis results.
+          pattern: "methurator_*.yml"
+  versions:
+    - versions.yml:
+        type: file
+        description: |
+          File containing software versions
+        pattern: "versions.yml"
+authors:
+  - "@edogiuili"
+maintainers:
+  - "@edogiuili"

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

@@ -0,0 +1,78 @@
+nextflow_process {
+
+    name "Test Process METHURATOR_GTESTIMATOR"
+    script "../main.nf"
+    process "METHURATOR_GTESTIMATOR"
+
+    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 {
+                t_max = 10
+                minimum_coverage = 1
+                rrbs = false
+            }
+            process {
+                """
+                input[0] = [ [ id:'test_bam' ],
+                               file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = [ [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai')
+                ]
+                input[2] = [ [ id: 'test_fasta' ],
+                             file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.summary_report.size() == 1 },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("Run methurator gt-estimator on paired-end methylated [bam] | sarscov2 genome [fasta] - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                minimum_coverage = 1
+                t_max = 10
+                rrbs = false
+            }
+            process {
+                """
+                input[0] = [ [ id:'test_bam' ],
+                               file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = [ [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai')
+                ]
+                input[2] = [ [ id: 'test_fasta' ],
+                             file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.summary_report.size() == 1 },
+                { assert snapshot(process.out.versions).match("versions_stub") }
+            )
+        }
+    }
+}

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

@@ -0,0 +1,26 @@
+{
+    "versions_stub": {
+        "content": [
+            [
+                "versions.yml:md5,22b8f66df736ae7c456269f537532688"
+            ]
+        ],
+        "timestamp": "2026-04-01T18:22:15.772095",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.0"
+        }
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,22b8f66df736ae7c456269f537532688"
+            ]
+        ],
+        "timestamp": "2026-04-01T18:17:57.637285",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.0"
+        }
+    }
+}

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 +1,43 @@
+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
+    path "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+    methurator plot \\
+        --summary $summary_report \\
+        --outdir .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        methurator: "\$(methurator --version 2>&1 | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/')"
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "plots/${meta.id}.html"
+    """
+    mkdir plots/
+    touch ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        methurator: "\$(methurator --version 2>&1 | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/')"
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,53 @@
+name: methurator_plot
+description: Plots results produced by methurator.
+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 ]
+    - summary_report:
+        type: file
+        description: |
+          YAML file summarizing the saturation analysis results.
+        pattern: "methurator_*.yml"
+output:
+  plots:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "plots/*.html":
+          type: file
+          description: |
+            HTML plots generated from the saturation analysis.
+          pattern: "plots/*.html"
+  versions:
+    - versions.yml:
+        type: file
+        description: |
+          File containing software versions
+        pattern: "versions.yml"
+authors:
+  - "@edogiuili"
+maintainers:
+  - "@edogiuili"