From 16568e138ead6717f4fb27e604e4269bb95709eb Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Wed, 1 Apr 2026 18:31:02 +0200
Subject: [PATCH 01/19] add methurator gtestimator and plot modules

---
 .../methurator/gtestimator/environment.yml    |  7 ++
 .../nf-core/methurator/gtestimator/main.nf    | 52 +++++++++++++
 .../nf-core/methurator/gtestimator/meta.yml   | 71 +++++++++++++++++
 .../methurator/gtestimator/tests/main.nf.test | 78 +++++++++++++++++++
 .../gtestimator/tests/main.nf.test.snap       | 26 +++++++
 .../nf-core/methurator/plot/environment.yml   |  7 ++
 modules/nf-core/methurator/plot/main.nf       | 43 ++++++++++
 modules/nf-core/methurator/plot/meta.yml      | 53 +++++++++++++
 .../methurator/plot/tests/main.nf.test        | 77 ++++++++++++++++++
 .../methurator/plot/tests/main.nf.test.snap   | 26 +++++++
 10 files changed, 440 insertions(+)
 create mode 100644 modules/nf-core/methurator/gtestimator/environment.yml
 create mode 100644 modules/nf-core/methurator/gtestimator/main.nf
 create mode 100755 modules/nf-core/methurator/gtestimator/meta.yml
 create mode 100644 modules/nf-core/methurator/gtestimator/tests/main.nf.test
 create mode 100644 modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/methurator/plot/environment.yml
 create mode 100644 modules/nf-core/methurator/plot/main.nf
 create mode 100644 modules/nf-core/methurator/plot/meta.yml
 create mode 100644 modules/nf-core/methurator/plot/tests/main.nf.test
 create mode 100644 modules/nf-core/methurator/plot/tests/main.nf.test.snap

diff --git a/modules/nf-core/methurator/gtestimator/environment.yml b/modules/nf-core/methurator/gtestimator/environment.yml
new file mode 100644
index 000000000000..942a9948cb6d
--- /dev/null
+++ b/modules/nf-core/methurator/gtestimator/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::methurator=2.1.1"
diff --git a/modules/nf-core/methurator/gtestimator/main.nf b/modules/nf-core/methurator/gtestimator/main.nf
new file mode 100644
index 000000000000..2c63c00510a9
--- /dev/null
+++ b/modules/nf-core/methurator/gtestimator/main.nf
@@ -0,0 +1,52 @@
+process METHURATOR_GTESTIMATOR {
+    tag "$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
+    """
+}
diff --git a/modules/nf-core/methurator/gtestimator/meta.yml b/modules/nf-core/methurator/gtestimator/meta.yml
new file mode 100755
index 000000000000..07873d7e48c7
--- /dev/null
+++ b/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"
diff --git a/modules/nf-core/methurator/gtestimator/tests/main.nf.test b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
new file mode 100644
index 000000000000..e9f670b3617b
--- /dev/null
+++ b/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") }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap b/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
new file mode 100644
index 000000000000..ebe2634ec81a
--- /dev/null
+++ b/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"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/methurator/plot/environment.yml b/modules/nf-core/methurator/plot/environment.yml
new file mode 100644
index 000000000000..942a9948cb6d
--- /dev/null
+++ b/modules/nf-core/methurator/plot/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::methurator=2.1.1"
diff --git a/modules/nf-core/methurator/plot/main.nf b/modules/nf-core/methurator/plot/main.nf
new file mode 100644
index 000000000000..91643dce5651
--- /dev/null
+++ b/modules/nf-core/methurator/plot/main.nf
@@ -0,0 +1,43 @@
+process METHURATOR_PLOT {
+    tag "$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
+    """
+}
diff --git a/modules/nf-core/methurator/plot/meta.yml b/modules/nf-core/methurator/plot/meta.yml
new file mode 100644
index 000000000000..c9b9629af4bd
--- /dev/null
+++ b/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"
diff --git a/modules/nf-core/methurator/plot/tests/main.nf.test b/modules/nf-core/methurator/plot/tests/main.nf.test
new file mode 100644
index 000000000000..d1fb05cce6a2
--- /dev/null
+++ b/modules/nf-core/methurator/plot/tests/main.nf.test
@@ -0,0 +1,77 @@
+nextflow_process {
+
+    name "Test Process METHURATOR_PLOT"
+    script "../main.nf"
+    process "METHURATOR_PLOT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "methurator"
+    tag "methurator/plot"
+    tag "methurator/gtestimator"
+
+    setup {
+            run("METHURATOR_GTESTIMATOR") {
+                script "../../gtestimator/main.nf"
+                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)
+                ]
+                """
+                }
+            }
+        }
+
+    test("Run methurator plot on the output of methurator gt-estimator") {
+
+        when {
+            process {
+                """
+                input[0] = METHURATOR_GTESTIMATOR.out.summary_report
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("Run methurator plot on the output of methurator gt-estimator - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = METHURATOR_GTESTIMATOR.out.summary_report
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions_stub") }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/methurator/plot/tests/main.nf.test.snap b/modules/nf-core/methurator/plot/tests/main.nf.test.snap
new file mode 100644
index 000000000000..879f1c206a06
--- /dev/null
+++ b/modules/nf-core/methurator/plot/tests/main.nf.test.snap
@@ -0,0 +1,26 @@
+{
+    "versions_stub": {
+        "content": [
+            [
+                "versions.yml:md5,fe5385d3b0af362701076bf8738e51ff"
+            ]
+        ],
+        "timestamp": "2026-04-01T18:22:44.204721",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.0"
+        }
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,fe5385d3b0af362701076bf8738e51ff"
+            ]
+        ],
+        "timestamp": "2026-04-01T18:18:21.803755",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.0"
+        }
+    }
+}
\ No newline at end of file

From d1089a4fd6fb8d6188afee1fa0cadc2956df19d2 Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Thu, 2 Apr 2026 23:51:30 +0200
Subject: [PATCH 02/19] add sanitizeOutput and snapshot on summary_report
 content

---
 .../methurator/gtestimator/tests/main.nf.test        | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/methurator/gtestimator/tests/main.nf.test b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
index e9f670b3617b..8d63bc6933d6 100644
--- a/modules/nf-core/methurator/gtestimator/tests/main.nf.test
+++ b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
@@ -35,13 +35,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert process.out.summary_report.size() == 1 },
-                { assert snapshot(process.out.versions).match("versions") }
+                { 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],
+                    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"
@@ -70,8 +71,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert process.out.summary_report.size() == 1 },
-                { assert snapshot(process.out.versions).match("versions_stub") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

From c8cf29c7cc65bd6338f2126a3ed68d300e379f9a Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Thu, 2 Apr 2026 23:52:01 +0200
Subject: [PATCH 03/19] add sanitizeOutput and snapshot on summary_report
 content

---
 modules/nf-core/methurator/gtestimator/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/methurator/gtestimator/tests/main.nf.test b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
index 8d63bc6933d6..3bada798d2cb 100644
--- a/modules/nf-core/methurator/gtestimator/tests/main.nf.test
+++ b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
@@ -39,7 +39,7 @@ nextflow_process {
                     // 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],
                     process.out.findAll { key, val -> key.startsWith('versions') }
-                ).match() }
+                ).match()}
             )
         }
     }

From 0234675f806a2b602cb91f8c9cd63953a88be0af Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Thu, 2 Apr 2026 23:53:41 +0200
Subject: [PATCH 04/19] update versions output to utilize topics and
 chanuniform name summary report with methurator_summary

---
 .../nf-core/methurator/gtestimator/main.nf    | 33 ++++++++-----------
 1 file changed, 13 insertions(+), 20 deletions(-)
 mode change 100644 => 100755 modules/nf-core/methurator/gtestimator/main.nf

diff --git a/modules/nf-core/methurator/gtestimator/main.nf b/modules/nf-core/methurator/gtestimator/main.nf
old mode 100644
new mode 100755
index 2c63c00510a9..a0ab41140cf2
--- a/modules/nf-core/methurator/gtestimator/main.nf
+++ b/modules/nf-core/methurator/gtestimator/main.nf
@@ -1,11 +1,11 @@
 process METHURATOR_GTESTIMATOR {
-    tag "$meta.id"
+    tag "${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' }"
+    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)
@@ -13,40 +13,33 @@ process METHURATOR_GTESTIMATOR {
     tuple val(meta3), path(fasta)
 
     output:
-    tuple val(meta), path("methurator_*.yml")    , emit: summary_report
-    path  "versions.yml"                         , emit: versions
+    tuple val(meta), path("methurator_summary.yml"), emit: summary_report
+    tuple val("${task.process}"), val('methurator'), eval('methurator --version'), emit: versions_methurator, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    if(params.rrbs) { args += '--rrbs'}
+    if (params.rrbs) {
+        args += '--rrbs'
+    }
     """
     methurator gt-estimator \\
-        $bam \\
-        --fasta $fasta \\
+        ${bam} \\
+        --fasta ${fasta} \\
         --minimum-coverage ${params.minimum_coverage} \\
         --t-max ${params.t_max} \\
         -@ ${task.cpus} \\
         --outdir . \\
         --compute_ci \\
-        $args
+        ${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
+    touch methurator_summary.yml
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        methurator: "\$(methurator --version 2>&1 | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/')"
-    END_VERSIONS
     """
 }

From df43d78ca6b385b849671102f9f098d5087f67fb Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Thu, 2 Apr 2026 23:55:53 +0200
Subject: [PATCH 05/19] add ontologies, make the description more specific, add
 topics

---
 .../nf-core/methurator/gtestimator/meta.yml   | 40 ++++++++++++++-----
 1 file changed, 29 insertions(+), 11 deletions(-)

diff --git a/modules/nf-core/methurator/gtestimator/meta.yml b/modules/nf-core/methurator/gtestimator/meta.yml
index 07873d7e48c7..70d5538daaf0 100755
--- a/modules/nf-core/methurator/gtestimator/meta.yml
+++ b/modules/nf-core/methurator/gtestimator/meta.yml
@@ -1,7 +1,6 @@
 name: methurator_gtestimator
 description: |
-  Methurator is a Python package designed to estimate CpGs saturation
-  for DNA methylation sequencing data.
+  Run estimator for DNA methylation sequencing saturation.
 keywords:
   - rrbs
   - BS-seq
@@ -17,7 +16,8 @@ tools:
         for DNA methylation sequencing data.
       homepage: https://github.com/VIBTOBIlab/methurator
       documentation: https://github.com/VIBTOBIlab/methurator/README.md
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -29,6 +29,7 @@ input:
         type: file
         description: BAM/CRAM file
         pattern: "*.{bam,cram}"
+        ontologies: []
   - - meta2:
         type: map
         description: |
@@ -38,6 +39,7 @@ input:
         type: file
         description: BAM/CRAM index file
         pattern: "*.{bai,crai}"
+        ontologies: []
   - - meta3:
         type: map
         description: |
@@ -47,6 +49,7 @@ input:
         type: file
         description: Input genome fasta file
         pattern: "*.{fasta,fa}"
+        ontologies: []
 output:
   summary_report:
     - - meta:
@@ -54,17 +57,32 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "methurator_*.yml":
+      - methurator_summary.yml:
           type: file
           description: |
-            YAML file summarizing the saturation analysis results.
-          pattern: "methurator_*.yml"
+            methurator gtestimator summary report in YAML format
+          ontologies: []
+  versions_methurator:
+    - - ${task.process}:
+          type: string
+          description: methurator gtestimator
+      - methurator:
+          type: string
+          description: methurator
+      - methurator --version:
+          type: eval
+          description: methurator software versions
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: |
-          File containing software versions
-        pattern: "versions.yml"
+    - - ${task.process}:
+          type: string
+          description: methurator gtestimator
+      - methurator:
+          type: string
+          description: methurator
+      - methurator --version:
+          type: eval
+          description: methurator software versions
 authors:
   - "@edogiuili"
 maintainers:

From 888568422b06a98aa65d3635c28104aeff674353 Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Thu, 2 Apr 2026 23:57:03 +0200
Subject: [PATCH 06/19] add snapshots on the file name and sanitizeOutput

---
 modules/nf-core/methurator/plot/tests/main.nf.test | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/methurator/plot/tests/main.nf.test b/modules/nf-core/methurator/plot/tests/main.nf.test
index d1fb05cce6a2..1d3bfe4353da 100644
--- a/modules/nf-core/methurator/plot/tests/main.nf.test
+++ b/modules/nf-core/methurator/plot/tests/main.nf.test
@@ -47,10 +47,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(
+                    process.out.plots.collect { it.collect { it instanceof Map ? it : file(it).name } },
+                    process.out.findAll { key, val -> key.startsWith('versions') }).match()
+                }
             )
         }
-
     }
 
     test("Run methurator plot on the output of methurator gt-estimator - stub") {
@@ -68,7 +70,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match("versions_stub") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
 

From 6a27790519c25ab17e2dc7ca9a1da9f1f9d59f45 Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Thu, 2 Apr 2026 23:57:21 +0200
Subject: [PATCH 07/19] add snapshots on the file name and sanitizeOutput

---
 modules/nf-core/methurator/plot/tests/main.nf.test | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/nf-core/methurator/plot/tests/main.nf.test b/modules/nf-core/methurator/plot/tests/main.nf.test
index 1d3bfe4353da..1b5228f40c76 100644
--- a/modules/nf-core/methurator/plot/tests/main.nf.test
+++ b/modules/nf-core/methurator/plot/tests/main.nf.test
@@ -73,7 +73,5 @@ nextflow_process {
                 { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
-
 }

From 622022f26a878514bbe3b459d878be4a0d8c385c Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Thu, 2 Apr 2026 23:58:20 +0200
Subject: [PATCH 08/19] add topics, lint the process

---
 modules/nf-core/methurator/plot/main.nf | 26 +++++++++----------------
 1 file changed, 9 insertions(+), 17 deletions(-)

diff --git a/modules/nf-core/methurator/plot/main.nf b/modules/nf-core/methurator/plot/main.nf
index 91643dce5651..2910daebaa1f 100644
--- a/modules/nf-core/methurator/plot/main.nf
+++ b/modules/nf-core/methurator/plot/main.nf
@@ -1,18 +1,18 @@
 process METHURATOR_PLOT {
-    tag "$meta.id"
+    tag "${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' }"
+    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
+    tuple val(meta), path("plots/*.html"), emit: plots
+    tuple val("${task.process}"), val('methurator'), eval('methurator --version'), emit: versions_methurator, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,24 +20,16 @@ process METHURATOR_PLOT {
     script:
     """
     methurator plot \\
-        --summary $summary_report \\
+        --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/${meta.id}.html"
+    def prefix = task.ext.prefix ?: "${meta.id}.html"
     """
     mkdir plots/
-    touch ${prefix}
+    touch plots/${prefix}
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        methurator: "\$(methurator --version 2>&1 | sed -E 's/.*version[[:space:]]+([0-9.]+).*/\\1/')"
-    END_VERSIONS
     """
 }

From 670437cc65d3063b63cc422efe748b18911d1a3f Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Thu, 2 Apr 2026 23:59:20 +0200
Subject: [PATCH 09/19] add topics, update output, update description, add
 ontologies

---
 modules/nf-core/methurator/plot/meta.yml | 35 ++++++++++++++++++------
 1 file changed, 27 insertions(+), 8 deletions(-)

diff --git a/modules/nf-core/methurator/plot/meta.yml b/modules/nf-core/methurator/plot/meta.yml
index c9b9629af4bd..69c1e8d4562c 100644
--- a/modules/nf-core/methurator/plot/meta.yml
+++ b/modules/nf-core/methurator/plot/meta.yml
@@ -1,5 +1,5 @@
 name: methurator_plot
-description: Plots results produced by methurator.
+description: Plots results produced by methurator gtestimator.
 keywords:
   - rrbs
   - BS-seq
@@ -16,7 +16,8 @@ tools:
         for DNA methylation sequencing data.
       homepage: https://github.com/VIBTOBIlab/methurator
       documentation: https://github.com/VIBTOBIlab/methurator/README.md
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -29,6 +30,8 @@ input:
         description: |
           YAML file summarizing the saturation analysis results.
         pattern: "methurator_*.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
 output:
   plots:
     - - meta:
@@ -36,17 +39,33 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "plots/*.html":
+      - plots/*.html:
           type: file
           description: |
             HTML plots generated from the saturation analysis.
           pattern: "plots/*.html"
+          ontologies: []
+  versions_methurator:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - methurator:
+          type: string
+          description: The name of the tool
+      - methurator --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: |
-          File containing software versions
-        pattern: "versions.yml"
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - methurator:
+          type: string
+          description: The name of the tool
+      - methurator --version:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@edogiuili"
 maintainers:

From c992f4ad0bd28495822bb821c91608eafae395d4 Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Thu, 2 Apr 2026 23:59:38 +0200
Subject: [PATCH 10/19] update snaps

---
 .../gtestimator/tests/main.nf.test.snap       | 48 +++++++++++++++----
 .../methurator/plot/tests/main.nf.test.snap   | 46 ++++++++++++++----
 2 files changed, 76 insertions(+), 18 deletions(-)

diff --git a/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap b/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
index ebe2634ec81a..5ec06a166a44 100644
--- a/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
+++ b/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
@@ -1,23 +1,53 @@
 {
-    "versions_stub": {
+    "Run methurator gt-estimator on paired-end methylated [bam] | sarscov2 genome [fasta] - stub": {
         "content": [
-            [
-                "versions.yml:md5,22b8f66df736ae7c456269f537532688"
-            ]
+            {
+                "summary_report": [
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "methurator_summary.yml:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_methurator": [
+                    [
+                        "METHURATOR_GTESTIMATOR",
+                        "methurator",
+                        "methurator, version 2.1.1"
+                    ]
+                ]
+            }
         ],
-        "timestamp": "2026-04-01T18:22:15.772095",
+        "timestamp": "2026-04-02T23:42:39.24087",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"
         }
     },
-    "versions": {
+    "Run methurator gt-estimator on paired-end methylated [bam] | sarscov2 genome [fasta]": {
         "content": [
             [
-                "versions.yml:md5,22b8f66df736ae7c456269f537532688"
-            ]
+                "    methurator_version: 2.1.1",
+                "    command: methurator gt_estimator",
+                "    options:",
+                "      cov_files:",
+                "      - ./covs/test.paired_end.methylated.sorted_CpG.bedGraph.gz",
+                "      outdir: .",
+                "      minimum_coverage: '1'",
+                "      t_step: 0.05"
+            ],
+            {
+                "versions_methurator": [
+                    [
+                        "METHURATOR_GTESTIMATOR",
+                        "methurator",
+                        "methurator, version 2.1.1"
+                    ]
+                ]
+            }
         ],
-        "timestamp": "2026-04-01T18:17:57.637285",
+        "timestamp": "2026-04-02T15:49:50.342905",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"
diff --git a/modules/nf-core/methurator/plot/tests/main.nf.test.snap b/modules/nf-core/methurator/plot/tests/main.nf.test.snap
index 879f1c206a06..03434ad98874 100644
--- a/modules/nf-core/methurator/plot/tests/main.nf.test.snap
+++ b/modules/nf-core/methurator/plot/tests/main.nf.test.snap
@@ -1,23 +1,51 @@
 {
-    "versions_stub": {
+    "Run methurator plot on the output of methurator gt-estimator": {
         "content": [
             [
-                "versions.yml:md5,fe5385d3b0af362701076bf8738e51ff"
-            ]
+                [
+                    {
+                        "id": "test_bam"
+                    },
+                    "test.paired_end.methylated.sorted_CpG.bedGraph_1x_plot.html"
+                ]
+            ],
+            {
+                "versions_methurator": [
+                    [
+                        "METHURATOR_PLOT",
+                        "methurator",
+                        "methurator, version 2.1.1"
+                    ]
+                ]
+            }
         ],
-        "timestamp": "2026-04-01T18:22:44.204721",
+        "timestamp": "2026-04-02T19:34:24.912049",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"
         }
     },
-    "versions": {
+    "Run methurator plot on the output of methurator gt-estimator - stub": {
         "content": [
-            [
-                "versions.yml:md5,fe5385d3b0af362701076bf8738e51ff"
-            ]
+            {
+                "plots": [
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_methurator": [
+                    [
+                        "METHURATOR_PLOT",
+                        "methurator",
+                        "methurator, version 2.1.1"
+                    ]
+                ]
+            }
         ],
-        "timestamp": "2026-04-01T18:18:21.803755",
+        "timestamp": "2026-04-02T17:04:03.284",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"

From 083231d7bfe24d1ce7fa63fa2bf41f726853b307 Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Sat, 4 Apr 2026 18:02:47 +0200
Subject: [PATCH 11/19] change the expression in eval to output just version
 number

---
 modules/nf-core/methurator/gtestimator/main.nf       |  2 +-
 modules/nf-core/methurator/gtestimator/meta.yml      | 12 ++++++------
 .../methurator/gtestimator/tests/main.nf.test.snap   |  8 ++++----
 modules/nf-core/methurator/plot/main.nf              |  2 +-
 modules/nf-core/methurator/plot/meta.yml             |  8 ++++----
 .../nf-core/methurator/plot/tests/main.nf.test.snap  |  8 ++++----
 6 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/modules/nf-core/methurator/gtestimator/main.nf b/modules/nf-core/methurator/gtestimator/main.nf
index a0ab41140cf2..bda54e93edf7 100755
--- a/modules/nf-core/methurator/gtestimator/main.nf
+++ b/modules/nf-core/methurator/gtestimator/main.nf
@@ -14,7 +14,7 @@ process METHURATOR_GTESTIMATOR {
 
     output:
     tuple val(meta), path("methurator_summary.yml"), emit: summary_report
-    tuple val("${task.process}"), val('methurator'), eval('methurator --version'), emit: versions_methurator, topic: versions
+    tuple val("${task.process}"), val('methurator'), eval("methurator --version | sed 's/.* //'"), emit: versions_methurator, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/methurator/gtestimator/meta.yml b/modules/nf-core/methurator/gtestimator/meta.yml
index 70d5538daaf0..32b76c8b0a0b 100755
--- a/modules/nf-core/methurator/gtestimator/meta.yml
+++ b/modules/nf-core/methurator/gtestimator/meta.yml
@@ -68,10 +68,10 @@ output:
           description: methurator gtestimator
       - methurator:
           type: string
-          description: methurator
-      - methurator --version:
+          description: The name of the tool
+      - methurator --version | sed 's/.* //':
           type: eval
-          description: methurator software versions
+          description: The expression to obtain the version of the tool
 topics:
   versions:
     - - ${task.process}:
@@ -79,10 +79,10 @@ topics:
           description: methurator gtestimator
       - methurator:
           type: string
-          description: methurator
-      - methurator --version:
+          description: The name of the tool
+      - methurator --version | sed 's/.* //':
           type: eval
-          description: methurator software versions
+          description: The expression to obtain the version of the tool
 authors:
   - "@edogiuili"
 maintainers:
diff --git a/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap b/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
index 5ec06a166a44..b2705b99dea2 100644
--- a/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
+++ b/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
@@ -14,12 +14,12 @@
                     [
                         "METHURATOR_GTESTIMATOR",
                         "methurator",
-                        "methurator, version 2.1.1"
+                        "2.1.1"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-04-02T23:42:39.24087",
+        "timestamp": "2026-04-04T17:56:55.555845",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"
@@ -42,12 +42,12 @@
                     [
                         "METHURATOR_GTESTIMATOR",
                         "methurator",
-                        "methurator, version 2.1.1"
+                        "2.1.1"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-04-02T15:49:50.342905",
+        "timestamp": "2026-04-04T17:56:48.448736",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"
diff --git a/modules/nf-core/methurator/plot/main.nf b/modules/nf-core/methurator/plot/main.nf
index 2910daebaa1f..d7563b1185e6 100644
--- a/modules/nf-core/methurator/plot/main.nf
+++ b/modules/nf-core/methurator/plot/main.nf
@@ -12,7 +12,7 @@ process METHURATOR_PLOT {
 
     output:
     tuple val(meta), path("plots/*.html"), emit: plots
-    tuple val("${task.process}"), val('methurator'), eval('methurator --version'), emit: versions_methurator, topic: versions
+    tuple val("${task.process}"), val('methurator'), eval("methurator --version | sed 's/.* //'"), emit: versions_methurator, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/methurator/plot/meta.yml b/modules/nf-core/methurator/plot/meta.yml
index 69c1e8d4562c..fe7b17499d3f 100644
--- a/modules/nf-core/methurator/plot/meta.yml
+++ b/modules/nf-core/methurator/plot/meta.yml
@@ -48,22 +48,22 @@ output:
   versions_methurator:
     - - ${task.process}:
           type: string
-          description: The name of the process
+          description: methurator plot
       - methurator:
           type: string
           description: The name of the tool
-      - methurator --version:
+      - methurator --version | sed 's/.* //':
           type: eval
           description: The expression to obtain the version of the tool
 topics:
   versions:
     - - ${task.process}:
           type: string
-          description: The name of the process
+          description: methurator plot
       - methurator:
           type: string
           description: The name of the tool
-      - methurator --version:
+      - methurator --version | sed 's/.* //':
           type: eval
           description: The expression to obtain the version of the tool
 authors:
diff --git a/modules/nf-core/methurator/plot/tests/main.nf.test.snap b/modules/nf-core/methurator/plot/tests/main.nf.test.snap
index 03434ad98874..18c351ef696c 100644
--- a/modules/nf-core/methurator/plot/tests/main.nf.test.snap
+++ b/modules/nf-core/methurator/plot/tests/main.nf.test.snap
@@ -14,12 +14,12 @@
                     [
                         "METHURATOR_PLOT",
                         "methurator",
-                        "methurator, version 2.1.1"
+                        "2.1.1"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-04-02T19:34:24.912049",
+        "timestamp": "2026-04-04T17:57:10.580629",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"
@@ -40,12 +40,12 @@
                     [
                         "METHURATOR_PLOT",
                         "methurator",
-                        "methurator, version 2.1.1"
+                        "2.1.1"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-04-02T17:04:03.284",
+        "timestamp": "2026-04-04T17:57:21.322182",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"

From 2d1c6db5306542f24b5a0871b1cf585b324ab871 Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Tue, 7 Apr 2026 14:51:10 +0200
Subject: [PATCH 12/19] add .join().md5 as suggested

---
 .../methurator/gtestimator/tests/main.nf.test     |  2 +-
 .../gtestimator/tests/main.nf.test.snap           | 15 +++------------
 2 files changed, 4 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/methurator/gtestimator/tests/main.nf.test b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
index 3bada798d2cb..4e5507308710 100644
--- a/modules/nf-core/methurator/gtestimator/tests/main.nf.test
+++ b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
@@ -37,7 +37,7 @@ nextflow_process {
                 { 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],
+                    file(process.out.summary_report[0][1]).readLines()[3..10].join('\n').md5(),
                     process.out.findAll { key, val -> key.startsWith('versions') }
                 ).match()}
             )
diff --git a/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap b/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
index b2705b99dea2..527590e12264 100644
--- a/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
+++ b/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-04T17:56:55.555845",
+        "timestamp": "2026-04-07T14:33:34.389842",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"
@@ -27,16 +27,7 @@
     },
     "Run methurator gt-estimator on paired-end methylated [bam] | sarscov2 genome [fasta]": {
         "content": [
-            [
-                "    methurator_version: 2.1.1",
-                "    command: methurator gt_estimator",
-                "    options:",
-                "      cov_files:",
-                "      - ./covs/test.paired_end.methylated.sorted_CpG.bedGraph.gz",
-                "      outdir: .",
-                "      minimum_coverage: '1'",
-                "      t_step: 0.05"
-            ],
+            "983d27e4d62f86d15a779820758af458",
             {
                 "versions_methurator": [
                     [
@@ -47,7 +38,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-04T17:56:48.448736",
+        "timestamp": "2026-04-07T14:33:27.127158",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"

From 74ecd84d94f120ae5e8ce10e5be61c6f5b763e6a Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Tue, 7 Apr 2026 14:51:25 +0200
Subject: [PATCH 13/19] update test

---
 modules/nf-core/methurator/plot/tests/main.nf.test.snap | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/methurator/plot/tests/main.nf.test.snap b/modules/nf-core/methurator/plot/tests/main.nf.test.snap
index 18c351ef696c..8202a599255c 100644
--- a/modules/nf-core/methurator/plot/tests/main.nf.test.snap
+++ b/modules/nf-core/methurator/plot/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-04T17:57:10.580629",
+        "timestamp": "2026-04-07T14:33:51.151509",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"
@@ -45,7 +45,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-04T17:57:21.322182",
+        "timestamp": "2026-04-07T14:34:01.714635",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"

From 26b2bca468eff3aff0d124254935dd60e7c7569f Mon Sep 17 00:00:00 2001
From: Edoardo <85080683+edogiuili@users.noreply.github.com>
Date: Tue, 7 Apr 2026 18:18:11 +0200
Subject: [PATCH 14/19] Update main.nf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
---
 modules/nf-core/methurator/plot/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/methurator/plot/main.nf b/modules/nf-core/methurator/plot/main.nf
index d7563b1185e6..cd71379f280b 100644
--- a/modules/nf-core/methurator/plot/main.nf
+++ b/modules/nf-core/methurator/plot/main.nf
@@ -29,7 +29,7 @@ process METHURATOR_PLOT {
     def prefix = task.ext.prefix ?: "${meta.id}.html"
     """
     mkdir plots/
-    touch plots/${prefix}
+    touch plots/${prefix}.html
 
     """
 }

From 60ab8939781daf1fc073f5c76f3f4352ab82668a Mon Sep 17 00:00:00 2001
From: Edoardo <85080683+edogiuili@users.noreply.github.com>
Date: Tue, 7 Apr 2026 18:18:29 +0200
Subject: [PATCH 15/19] Update main.nf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
---
 modules/nf-core/methurator/plot/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/methurator/plot/main.nf b/modules/nf-core/methurator/plot/main.nf
index cd71379f280b..f079093cc5ca 100644
--- a/modules/nf-core/methurator/plot/main.nf
+++ b/modules/nf-core/methurator/plot/main.nf
@@ -26,7 +26,7 @@ process METHURATOR_PLOT {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}.html"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir plots/
     touch plots/${prefix}.html

From 4e1d5eec602c70afc0a505d1ea0e40f0f3b62bb5 Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Tue, 7 Apr 2026 22:48:39 +0200
Subject: [PATCH 16/19] put all the inputs into one tuple and add ontologies

---
 .../nf-core/methurator/gtestimator/main.nf    | 11 +++++----
 .../nf-core/methurator/gtestimator/meta.yml   | 21 ++++++----------
 .../methurator/gtestimator/tests/main.nf.test | 24 +++++++------------
 .../gtestimator/tests/main.nf.test.snap       |  7 +++---
 4 files changed, 25 insertions(+), 38 deletions(-)

diff --git a/modules/nf-core/methurator/gtestimator/main.nf b/modules/nf-core/methurator/gtestimator/main.nf
index bda54e93edf7..0307b39b1f8b 100755
--- a/modules/nf-core/methurator/gtestimator/main.nf
+++ b/modules/nf-core/methurator/gtestimator/main.nf
@@ -8,12 +8,10 @@ process METHURATOR_GTESTIMATOR {
         : 'biocontainers/methurator:2.1.1--pyhdfd78af_0'}"
 
     input:
-    tuple val(meta), path(bam)
-    tuple val(meta2), path(bai)
-    tuple val(meta3), path(fasta)
+    tuple val(meta), path(bam), path(bai), path(fasta)
 
     output:
-    tuple val(meta), path("methurator_summary.yml"), emit: summary_report
+    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:
@@ -24,6 +22,7 @@ process METHURATOR_GTESTIMATOR {
     if (params.rrbs) {
         args += '--rrbs'
     }
+    prefix = task.ext.prefix?: "${meta.id}"
     """
     methurator gt-estimator \\
         ${bam} \\
@@ -35,11 +34,13 @@ process METHURATOR_GTESTIMATOR {
         --compute_ci \\
         ${args}
 
+    mv methurator_summary.yml ${prefix}.yml
     """
 
     stub:
+    prefix = task.ext.prefix?: "${meta.id}"
     """
-    touch methurator_summary.yml
+    touch ${prefix}.yml
 
     """
 }
diff --git a/modules/nf-core/methurator/gtestimator/meta.yml b/modules/nf-core/methurator/gtestimator/meta.yml
index 32b76c8b0a0b..0b40456c9b7e 100755
--- a/modules/nf-core/methurator/gtestimator/meta.yml
+++ b/modules/nf-core/methurator/gtestimator/meta.yml
@@ -25,26 +25,17 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
+        ontologies: []
     - bam:
         type: file
-        description: BAM/CRAM file
+        description: Single BAM file
         pattern: "*.{bam,cram}"
         ontologies: []
-  - - meta2:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
     - bai:
         type: file
-        description: BAM/CRAM index file
+        description: Single BAM/CRAM index file
         pattern: "*.{bai,crai}"
         ontologies: []
-  - - meta3:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
     - fasta:
         type: file
         description: Input genome fasta file
@@ -57,10 +48,12 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - methurator_summary.yml:
+          ontologies: []
+      - "${prefix}.yml":
           type: file
           description: |
-            methurator gtestimator summary report in YAML format
+            YAML file summarizing the saturation analysis results.
+          pattern: "${prefix}.yml"
           ontologies: []
   versions_methurator:
     - - ${task.process}:
diff --git a/modules/nf-core/methurator/gtestimator/tests/main.nf.test b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
index 4e5507308710..4fbee0155822 100644
--- a/modules/nf-core/methurator/gtestimator/tests/main.nf.test
+++ b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
@@ -19,14 +19,10 @@ nextflow_process {
             }
             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)
+                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)
                 ]
                 """
             }
@@ -55,14 +51,10 @@ nextflow_process {
             }
             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)
+                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)
                 ]
                 """
             }
diff --git a/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap b/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
index 527590e12264..6e5d5ab3639f 100644
--- a/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
+++ b/modules/nf-core/methurator/gtestimator/tests/main.nf.test.snap
@@ -5,9 +5,10 @@
                 "summary_report": [
                     [
                         {
-                            "id": "test_bam"
+                            "id": "test",
+                            "single_end": false
                         },
-                        "methurator_summary.yml:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.yml:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions_methurator": [
@@ -19,7 +20,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-07T14:33:34.389842",
+        "timestamp": "2026-04-07T22:41:16.975667",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"

From b8218c051993fa9709831a7825ab99e1ddc98f8c Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Tue, 7 Apr 2026 22:49:48 +0200
Subject: [PATCH 17/19] put inputs into one tuple and minor changes

---
 modules/nf-core/methurator/plot/meta.yml             |  2 ++
 modules/nf-core/methurator/plot/tests/main.nf.test   | 12 ++++--------
 .../nf-core/methurator/plot/tests/main.nf.test.snap  | 12 +++++++-----
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/methurator/plot/meta.yml b/modules/nf-core/methurator/plot/meta.yml
index fe7b17499d3f..630067d1008c 100644
--- a/modules/nf-core/methurator/plot/meta.yml
+++ b/modules/nf-core/methurator/plot/meta.yml
@@ -25,6 +25,7 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
+        ontologies: []
     - summary_report:
         type: file
         description: |
@@ -39,6 +40,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
+          ontologies: []
       - plots/*.html:
           type: file
           description: |
diff --git a/modules/nf-core/methurator/plot/tests/main.nf.test b/modules/nf-core/methurator/plot/tests/main.nf.test
index 1b5228f40c76..acd4043937f1 100644
--- a/modules/nf-core/methurator/plot/tests/main.nf.test
+++ b/modules/nf-core/methurator/plot/tests/main.nf.test
@@ -20,14 +20,10 @@ nextflow_process {
                 }
                 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)
+                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)
                 ]
                 """
                 }
diff --git a/modules/nf-core/methurator/plot/tests/main.nf.test.snap b/modules/nf-core/methurator/plot/tests/main.nf.test.snap
index 8202a599255c..a52140b74c25 100644
--- a/modules/nf-core/methurator/plot/tests/main.nf.test.snap
+++ b/modules/nf-core/methurator/plot/tests/main.nf.test.snap
@@ -4,7 +4,8 @@
             [
                 [
                     {
-                        "id": "test_bam"
+                        "id": "test",
+                        "single_end": false
                     },
                     "test.paired_end.methylated.sorted_CpG.bedGraph_1x_plot.html"
                 ]
@@ -19,7 +20,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-07T14:33:51.151509",
+        "timestamp": "2026-04-07T22:44:11.302149",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"
@@ -31,9 +32,10 @@
                 "plots": [
                     [
                         {
-                            "id": "test_bam"
+                            "id": "test",
+                            "single_end": false
                         },
-                        "test_bam.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions_methurator": [
@@ -45,7 +47,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-07T14:34:01.714635",
+        "timestamp": "2026-04-07T22:44:22.201627",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.0"

From e75b482a76cb23d1cbd6ed8cb79d45739c7e02d5 Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Fri, 10 Apr 2026 11:25:51 +0200
Subject: [PATCH 18/19] move args and params to the task.ext.args and make a
 nextflow.config file for the test

---
 modules/nf-core/methurator/gtestimator/main.nf         |  8 +-------
 .../nf-core/methurator/gtestimator/tests/main.nf.test  |  3 +++
 .../methurator/gtestimator/tests/nextflow.config       | 10 ++++++++++
 3 files changed, 14 insertions(+), 7 deletions(-)
 create mode 100644 modules/nf-core/methurator/gtestimator/tests/nextflow.config

diff --git a/modules/nf-core/methurator/gtestimator/main.nf b/modules/nf-core/methurator/gtestimator/main.nf
index 0307b39b1f8b..cf64e35a881e 100755
--- a/modules/nf-core/methurator/gtestimator/main.nf
+++ b/modules/nf-core/methurator/gtestimator/main.nf
@@ -19,19 +19,13 @@ process METHURATOR_GTESTIMATOR {
 
     script:
     def args = task.ext.args ?: ''
-    if (params.rrbs) {
-        args += '--rrbs'
-    }
-    prefix = task.ext.prefix?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     methurator gt-estimator \\
         ${bam} \\
         --fasta ${fasta} \\
-        --minimum-coverage ${params.minimum_coverage} \\
-        --t-max ${params.t_max} \\
         -@ ${task.cpus} \\
         --outdir . \\
-        --compute_ci \\
         ${args}
 
     mv methurator_summary.yml ${prefix}.yml
diff --git a/modules/nf-core/methurator/gtestimator/tests/main.nf.test b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
index 4fbee0155822..38c621f44949 100644
--- a/modules/nf-core/methurator/gtestimator/tests/main.nf.test
+++ b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
@@ -3,6 +3,7 @@ nextflow_process {
     name "Test Process METHURATOR_GTESTIMATOR"
     script "../main.nf"
     process "METHURATOR_GTESTIMATOR"
+    config './nextflow.config'
 
     tag "modules"
     tag "modules_nfcore"
@@ -15,6 +16,7 @@ nextflow_process {
             params {
                 t_max = 10
                 minimum_coverage = 1
+                compute_ci = true
                 rrbs = false
             }
             process {
@@ -47,6 +49,7 @@ nextflow_process {
             params {
                 minimum_coverage = 1
                 t_max = 10
+                compute_ci = true
                 rrbs = false
             }
             process {
diff --git a/modules/nf-core/methurator/gtestimator/tests/nextflow.config b/modules/nf-core/methurator/gtestimator/tests/nextflow.config
new file mode 100644
index 000000000000..7748c17ff65d
--- /dev/null
+++ b/modules/nf-core/methurator/gtestimator/tests/nextflow.config
@@ -0,0 +1,10 @@
+process {
+    withName: METHURATOR_GTESTIMATOR {
+        ext.args = { [
+            params.rrbs ? '--rrbs' : '',
+            params.compute_ci ? ' --compute_ci' : '',
+            params.t_max ? " --t-max ${params.t_max}" : '',
+            params.minimum_coverage ? " --minimum-coverage ${params.minimum_coverage}" : ''
+        ].join(' ').trim() }
+    }
+}

From 9c8326025e1c35219536eb06ebaf375d68beabc0 Mon Sep 17 00:00:00 2001
From: edogiuili <edoardogiuili@gmail.com>
Date: Fri, 10 Apr 2026 13:15:59 +0200
Subject: [PATCH 19/19] move args into module_args param

---
 .../nf-core/methurator/gtestimator/tests/main.nf.test | 11 +++--------
 .../methurator/gtestimator/tests/nextflow.config      |  7 +------
 2 files changed, 4 insertions(+), 14 deletions(-)

diff --git a/modules/nf-core/methurator/gtestimator/tests/main.nf.test b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
index 38c621f44949..de1cff6e2687 100644
--- a/modules/nf-core/methurator/gtestimator/tests/main.nf.test
+++ b/modules/nf-core/methurator/gtestimator/tests/main.nf.test
@@ -14,11 +14,9 @@ nextflow_process {
 
         when {
             params {
-                t_max = 10
-                minimum_coverage = 1
-                compute_ci = true
-                rrbs = false
+                module_args = '--t-max 10 --minimum-coverage 1 --compute_ci'
             }
+
             process {
                 """
                 input[0] = [ [ id:'test', single_end:false ],
@@ -47,10 +45,7 @@ nextflow_process {
 
         when {
             params {
-                minimum_coverage = 1
-                t_max = 10
-                compute_ci = true
-                rrbs = false
+                module_args = '--t-max 10 --minimum-coverage 1 --compute_ci'
             }
             process {
                 """
diff --git a/modules/nf-core/methurator/gtestimator/tests/nextflow.config b/modules/nf-core/methurator/gtestimator/tests/nextflow.config
index 7748c17ff65d..9cb31eb3a925 100644
--- a/modules/nf-core/methurator/gtestimator/tests/nextflow.config
+++ b/modules/nf-core/methurator/gtestimator/tests/nextflow.config
@@ -1,10 +1,5 @@
 process {
     withName: METHURATOR_GTESTIMATOR {
-        ext.args = { [
-            params.rrbs ? '--rrbs' : '',
-            params.compute_ci ? ' --compute_ci' : '',
-            params.t_max ? " --t-max ${params.t_max}" : '',
-            params.minimum_coverage ? " --minimum-coverage ${params.minimum_coverage}" : ''
-        ].join(' ').trim() }
+        ext.args = params.module_args
     }
 }