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update cnvkit to reflect bug fixes #2051

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update cnvkit to reflect bug fixes #2051

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@bounlu
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@bounlu bounlu commented Nov 11, 2025 •
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update cnvkit to reflect bug fixes

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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

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8f715a4

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

❗ 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 2025-11-11 07:07:41

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SPPearce commented Nov 11, 2025

Hi @bounlu .
This change needs to be made first in https://github.com/nf-core/modules before it is propagated here.
That will involve changing the docker, singularity and conda definitions (the third through changing the environment.yml), as well as the nf-test snapshots (via nf-core modules test cnvkit/call -u).
Once it has been made there then it can be pulled into sarek via nf-core modules update, and the snapshots updated here.

@SPPearce SPPearce mentioned this pull request Nov 11, 2025
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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@bounlu @nf-core-bot @SPPearce @FriederikeHanssen