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Important! Template update for nf-core/tools v3.3.1 #1559

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pinin4fjords merged 11 commits into from
Jun 4, 2025
Merged

Important! Template update for nf-core/tools v3.3.1 #1559

pinin4fjords merged 11 commits into from
Jun 4, 2025

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@nf-core-bot nf-core-bot commented Jun 3, 2025

Version 3.3.1 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-3.3.1 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 v3.3.1 release page.

@nf-core-bot nf-core-bot mentioned this pull request Jun 3, 2025
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github-actions bot commented Jun 3, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6afadbb

+| ✅ 278 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-06-03 16:42:48

maxulysse
maxulysse reviewed Jun 3, 2025
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maxulysse
maxulysse reviewed Jun 3, 2025
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maxulysse
maxulysse reviewed Jun 3, 2025
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@pinin4fjords pinin4fjords merged commit 1675473 into dev Jun 4, 2025
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@pinin4fjords pinin4fjords deleted the nf-core-template-merge-3.3.1 branch June 4, 2025 09:48
@pinin4fjords pinin4fjords mentioned this pull request Jul 23, 2025
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@maxulysse maxulysse maxulysse approved these changes

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