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Important! Template update for nf-core/tools v3.4.1#880

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jfy133 merged 9 commits into
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nf-core-template-merge-3.4.1
Oct 23, 2025
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Important! Template update for nf-core/tools v3.4.1#880
jfy133 merged 9 commits into
devfrom
nf-core-template-merge-3.4.1

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@nf-core-bot

@nf-core-bot nf-core-bot commented Oct 16, 2025

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Version 3.4.1 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-3.4.1 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 v3.4.1 release page.

@nf-core-bot nf-core-bot mentioned this pull request Oct 16, 2025
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@jfy133 jfy133 self-assigned this Oct 17, 2025
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github-actions Bot commented Oct 17, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2380df0

+| ✅ 375 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • 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 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 nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-10-23 11:54:07

jfy133
jfy133 reviewed Oct 22, 2025
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Comment thread .github/workflows/release-announcements.yml Outdated
@jfy133

jfy133 commented Oct 23, 2025

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@nf-core-bot fix linting

@jfy133 jfy133 merged commit 23586dd into dev Oct 23, 2025
21 checks passed
@jfy133 jfy133 deleted the nf-core-template-merge-3.4.1 branch October 23, 2025 12:27
@jfy133 jfy133 mentioned this pull request Oct 25, 2025
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@jfy133 jfy133 jfy133 approved these changes

@mashehu mashehu mashehu approved these changes

@dialvarezs dialvarezs dialvarezs approved these changes

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

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

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

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