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fix: change yte input to one channel to disambiguate scenario file rendering #2053

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FriederikeHanssen merged 5 commits into from
Nov 18, 2025
Merged

fix: change yte input to one channel to disambiguate scenario file rendering #2053

FriederikeHanssen merged 5 commits into from
Nov 18, 2025

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@famosab
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@famosab famosab commented Nov 11, 2025 •
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@famosab famosab changed the title fix: change yte input to one channel to disambiguate scenario file re… fix: change yte input to one channel to disambiguate scenario file rendering Nov 11, 2025
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nf-core-bot commented Nov 11, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Nov 11, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fd4c887

+| ✅ 227 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: markduplicates_pixel_distance
  • schema_description - No description provided in schema for parameter: gatk_pcr_indel_model

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-11-12 21:12:05

FriederikeHanssen
FriederikeHanssen reviewed Nov 11, 2025
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modules/nf-core/yte/main.nf
tuple val(meta), path(template)
path(map_file)
val(map)
tuple val(meta), path(template), path(map_file), val(map)
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@FriederikeHanssen FriederikeHanssen Nov 11, 2025

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question
do we need two different maps here? Is there a reason what is in map cannot be added to the meta map?

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@famosab famosab Nov 11, 2025

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The way the module works it can accept two different maps and I think it makes sense to leave it that way because you do not want to set all variables in the "classic" meta map if you have a complex yte template. However for our case these are the same because its just two key-value-pairs that we easily extract from the classic meta map.

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famosab commented Nov 11, 2025

@FriederikeHanssen Now the tests ran and all is green yay

@FriederikeHanssen FriederikeHanssen merged commit f3a9511 into dev Nov 18, 2025
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@FriederikeHanssen FriederikeHanssen deleted the fix-yte branch November 18, 2025 09:17
@FriederikeHanssen FriederikeHanssen mentioned this pull request Dec 2, 2025
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@maxulysse maxulysse maxulysse approved these changes

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