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Prepare genome refactor #1979

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Merged
FriederikeHanssen merged 38 commits into from
Nov 3, 2025
Merged

Prepare genome refactor #1979

FriederikeHanssen merged 38 commits into from
Nov 3, 2025

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@maxulysse
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@maxulysse maxulysse commented Sep 10, 2025 •
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Pushing all the logic for reference files in the prepare_genome subworkflow to streamline the root main.nf script.
Hopefully that'll prepare for references at the same time

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).

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github-actions bot commented Sep 10, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit be35d5b

+| ✅ 226 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 2025-10-30 09:55:02

@maxulysse maxulysse mentioned this pull request Sep 11, 2025
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@maxulysse maxulysse marked this pull request as ready for review September 11, 2025 10:47
@maxulysse maxulysse mentioned this pull request Sep 16, 2025
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@edmundmiller edmundmiller self-requested a review September 17, 2025 14:36
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nf-core-bot commented Oct 15, 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.

maxulysse
maxulysse commented Oct 15, 2025
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maxulysse
maxulysse commented Oct 15, 2025
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maxulysse
maxulysse commented Oct 15, 2025
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maxulysse
maxulysse commented Oct 15, 2025
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maxulysse
maxulysse commented Oct 15, 2025
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maxulysse
maxulysse commented Oct 15, 2025
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FriederikeHanssen
FriederikeHanssen approved these changes Nov 3, 2025
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lgtm

@FriederikeHanssen FriederikeHanssen merged commit d17d30f into dev Nov 3, 2025
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@FriederikeHanssen FriederikeHanssen deleted the prepare_genome branch November 3, 2025 14:02
@jchchiu jchchiu mentioned this pull request Nov 13, 2025
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@FriederikeHanssen FriederikeHanssen mentioned this pull request Dec 2, 2025
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@matthdsm matthdsm matthdsm approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@edmundmiller edmundmiller Awaiting requested review from edmundmiller

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