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Prep 3.7.0 release#2057

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Prep 3.7.0 release#2057

FriederikeHanssen wants to merge1 commit intodevfromprep_37_release

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@FriederikeHanssen
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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 thecontribution docs
  • If necessary, also make a PR on the nf-core/sarekbranch on thenf-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 indocs/usage.md is updated.
  • Output Documentation indocs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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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 thenf-core documentation andSynchronisation documentation.

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github-actionsbot commentedNov 19, 2025•
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nf-core pipelines lint overall result: Passed ✅⚠️

Posted for pipeline commiteceaa10

+| ✅ 226 tests passed       |+#| ❔  13 tests were ignored |#!| ❗   8 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Configmanifest.version should end indev:3.7.0
  • pipeline_todos - TODO string inbase.config:Check the defaults for all processes
  • pipeline_todos - TODO string inmain.nf:Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string inmain.nf:Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string inmain.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 at2025-11-19 11:14:54

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@maxulyssemaxulysseAwaiting requested review from maxulyssemaxulysse will be requested when the pull request is marked ready for reviewmaxulysse is a code owner

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