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Important! Template update for nf-core/tools v3.3.1 #128

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Merged
famosab merged 7 commits into from
Jun 3, 2025
Merged

Important! Template update for nf-core/tools v3.3.1 #128

famosab merged 7 commits into from
Jun 3, 2025

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@nf-core-bot nf-core-bot commented Jun 2, 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.

famosab
famosab reviewed 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 d45b984

+| ✅ 239 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   9 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.2.0
  • 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 base.config: Check the defaults for all processes
  • local_component_structure - check_paired_end.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - prepare_indices.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - alignment_to_fastq.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - pre_conversion_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/ci.yml
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-06-03 09:28:09

@famosab famosab merged commit 3d1e65b into dev Jun 3, 2025
37 of 39 checks passed
@famosab famosab deleted the nf-core-template-merge-3.3.1 branch June 3, 2025 10:01
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@famosab famosab famosab approved these changes

@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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@nf-core-bot @famosab @mirpedrol