add methurator gtestimator and plot modules by edogiuili · Pull Request #11110 · nf-core/modules

edogiuili · 2026-04-01T16:48:44Z

In this PR, I add methurator gtestimator and plot modules.

PR checklist

famosab

Thank you for your contribution to nf-core! We really appreciate it. I added a few comments to your PR.

famosab · 2026-04-02T11:43:16Z

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

+
+    output:
+    tuple val(meta), path("methurator_*.yml")    , emit: summary_report
+    path  "versions.yml"                         , emit: versions


Can you update the versions output to utilize topics? More information about that can be found in the docs.

famosab · 2026-04-02T11:43:33Z

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

+    input:
+    tuple val(meta), path(bam)
+    tuple val(meta2), path(bai)
+    tuple val(meta3), path(fasta)


Can we put all these inputs into one tuple? That will make sure you're sure that EVERY time everything comes together in the right combination.

Since methurator uses MethylDackel inside, I sticked to the inputs that are present in MethylDackel nf-core module. Do you think it's still better to put them all into one tuple?

Its not something I will force you to do :D but its something we try to move towards to because it has some advantages (but it will be obsolete in the future with how nextflow will change its input syntax) so I would say this is up to you and keeping it consistent to methyldackel is a good argument to keep it like this

famosab · 2026-04-02T11:43:43Z

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

You can run

nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment

on this file to clean this up nicely.

famosab · 2026-04-02T11:44:51Z

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

+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "methurator_summary_${meta.id}"


Why is it called _summary here and in th output just merthurator?

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

famosab · 2026-04-02T11:48:20Z

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

See comments on above nf.test file

famosab · 2026-04-02T11:48:46Z

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

You can run

nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment

on this file to clean this up nicely.

famosab · 2026-04-02T11:48:57Z

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

+
+    output:
+    tuple val(meta), path("plots/*.html")  , emit: plots
+    path "versions.yml"                    , emit: versions


Can you update the versions output to utilize topics? More information about that can be found in the docs.

famosab · 2026-04-02T11:49:16Z

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

+    def prefix = task.ext.prefix ?: "plots/${meta.id}.html"
+    """
+    mkdir plots/
+    touch ${prefix}


Lets not create a dir if it only contains one output

This is necessary cause the process outputs the file into the plots/ folder, so I needed to create a file in that folder to avoid getting the following error in the stub:

Missing output file(s) `plots/*.html` expected by process `METHURATOR_PLOT (test_bam)

But maybe there is a more elegant way of doing this :D

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

… report with methurator_summary

edogiuili · 2026-04-02T22:22:03Z

Thanks for your suggestions Famke! I've addressed them all, apart from:

the inputs of methurator/gtestimator (for now)
the plots/ dir being created in the methurator/plot stub (find my answer here)

For the additional snapshots, instead of capturing the full files—which are unstable—I extracted a snapshot of the content from lines 3 to 9 for the methurator/gtestimator summary reports, and a snapshot of the HTML filename for the methurator plots. What do you think?

edogiuili · 2026-04-04T16:20:37Z

A small fix in the eval() expression to extract the software version. I changed the expression from methurator --version to methurator --version | sed 's/.* //' to only extract the version number (e.g. 2.1.1) and not the entire output (e.g. methurator, 2.1.1)

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

edogiuili · 2026-04-07T13:19:51Z

Hey Famke, I fixed the last suggestion you made, however, the nf-test seem to have run on files that are not related to this module, but rather to other modules. I do not know why this would happen 😕

famosab · 2026-04-07T16:03:21Z

Hey Famke, I fixed the last suggestion you made, however, the nf-test seem to have run on files that are not related to this module, but rather to other modules. I do not know why this would happen 😕

Happens because github -> you just need to merge the master branch then it only runs yours

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

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

famosab

I added a few more comments :)

famosab · 2026-04-07T18:28:31Z

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

+    tuple val(meta), path(bam)
+    tuple val(meta2), path(bai)
+    tuple val(meta3), path(fasta)


Can we put all these inputs into one tuple? That will make sure you're sure that EVERY time everything comes together in the right combination. At least bam and bai i would put in the same tuple. If the fasta does not change per input sample we can have it extra.

famosab · 2026-04-07T18:29:01Z

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

+    tuple val(meta3), path(fasta)
+
+    output:
+    tuple val(meta), path("methurator_summary.yml"), emit: summary_report


Can we somehow control the output name?

Suggested change

tuple val(meta), path("methurator_summary.yml"), emit: summary_report

tuple val(meta), path("${prefix}.yml"), emit: summary_report

famosab · 2026-04-07T18:29:28Z

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

+    def args = task.ext.args ?: ''
+    if (params.rrbs) {
+        args += '--rrbs'
+    }


Suggested change

}

}

prefix = task.ext.prefix?: "${meta.id}"

famosab · 2026-04-07T18:29:52Z

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

+        --outdir . \\
+        --compute_ci \\
+        ${args}
+


Suggested change

mv methurator_summary.yml ${prefix}.yml

famosab · 2026-04-07T18:30:07Z

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

+    stub:
+    """
+    touch methurator_summary.yml


And adjust it in the stub as well

famosab · 2026-04-07T18:30:25Z

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

+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM/CRAM file


can you be more specific, is only one bam allowed or can it be multiple?

The tool supports one or multiple BAM files, but within a Nextflow workflow I would only use 1 file at the time to enable parallel execution.

ok that would mean that via nextflow only one plot would be created downstream right? then we can maybe handle it differently in the plot module aswell?

It depends. If the --minimum-coverage parameter specified in the gtestimator module contains only 1 character (e.g. "3"), then yes. However, the users can specify more than 1 minimum coverage value (e.g. "1,3,5"), in which case one plot per minimum coverage value specified will be dumped in the plots/ folder.

ok maybe we can add this info to the meta map then but then its ok we leave it as is

famosab · 2026-04-07T18:31:20Z

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

Can you please add ontologies to the meta map?

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

famosab · 2026-04-07T18:32:50Z

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

+          description: |
+            HTML plots generated from the saturation analysis.
+          pattern: "plots/*.html"
+          ontologies: []


Can you please add ontologies to the meta map?

add methurator gtestimator and plot modules

16568e1

famosab reviewed Apr 2, 2026

View reviewed changes

edogiuili added 9 commits April 2, 2026 23:51

add sanitizeOutput and snapshot on summary_report content

d1089a4

add sanitizeOutput and snapshot on summary_report content

c8cf29c

update versions output to utilize topics and chanuniform name summary…

0234675

… report with methurator_summary

add ontologies, make the description more specific, add topics

df43d78

add snapshots on the file name and sanitizeOutput

8885684

add snapshots on the file name and sanitizeOutput

6a27790

add topics, lint the process

622022f

add topics, update output, update description, add ontologies

670437c

update snaps

c992f4a

change the expression in eval to output just version number

083231d

famosab reviewed Apr 7, 2026

View reviewed changes

modules/nf-core/methurator/gtestimator/tests/main.nf.test Outdated Show resolved Hide resolved

edogiuili added 2 commits April 7, 2026 14:51

add .join().md5 as suggested

2d1c6db

update test

74ecd84

Merge branch 'master' into methurator

236a062

famosab reviewed Apr 7, 2026

View reviewed changes

modules/nf-core/methurator/plot/main.nf Outdated Show resolved Hide resolved

modules/nf-core/methurator/plot/main.nf Outdated Show resolved Hide resolved

edogiuili and others added 2 commits April 7, 2026 18:18

Update main.nf

26b2bca

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

Update main.nf

60ab893

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

famosab reviewed Apr 7, 2026

View reviewed changes

edogiuili and others added 3 commits April 7, 2026 22:48

put all the inputs into one tuple and add ontologies

4e1d5ee

put inputs into one tuple and minor changes

b8218c0

Merge branch 'master' into methurator

e800259

	tuple val(meta), path("methurator_summary.yml"), emit: summary_report
	tuple val(meta), path("${prefix}.yml"), emit: summary_report

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edogiuili commented Apr 1, 2026

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edogiuili commented Apr 2, 2026

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