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Important! Template update for nf-core/tools v3.3.2 #253

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Merged
mirpedrol merged 7 commits into from
Jul 9, 2025
Merged

Important! Template update for nf-core/tools v3.3.2 #253

mirpedrol merged 7 commits into from
Jul 9, 2025

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@nf-core-bot nf-core-bot commented Jul 8, 2025

Version 3.3.2 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.3.2 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.3.2 release page.

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github-actions bot commented Jul 8, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 91b1eb2

+| ✅ 278 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  21 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • local_component_structure - clonality_classifier.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - cigar_parser.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - alignment_summary.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - find_adapters.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - hitselection.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - venndiagram.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - gpt_prepare_query.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - drugz.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - crisprseq_plotter.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - matricescreation.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - preprocessing_summary.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - orient_reference.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - template_reference.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - extract_umis.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - clustering_summary.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-07-09 08:13:46

@mirpedrol mirpedrol requested a review from matbonfanti July 8, 2025 10:24
matbonfanti
matbonfanti approved these changes Jul 9, 2025
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Hi @mirpedrol, thanks for taking care of this PR!

@mirpedrol mirpedrol merged commit 22d8902 into dev Jul 9, 2025
17 checks passed
@mirpedrol mirpedrol deleted the nf-core-template-merge-3.3.2 branch July 9, 2025 08:52
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@matbonfanti matbonfanti matbonfanti approved these changes

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