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Update to Nextflow 25.04 #1566

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bentsherman
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Minimal PR demonstrating how to use the latest features in Nextflow, including:

  • adhering to strict syntax
  • using topic channels and eval outputs to collect tool versions
  • replace publishDir with workflow outputs

None of these things are implemented completely, just wanted to show how to get started.

See also:

@nf-core-bot
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.0.
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.

@bentsherman bentsherman mentioned this pull request Jun 9, 2025
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github-actions bot commented Jun 9, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 20c3cc3

+| ✅ 278 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 3.19.0
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-06-09 04:13:46

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@bentsherman @nf-core-bot