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Update to Nextflow 25.04 #347

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bentsherman
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This PR updates the fetchngs pipeline to use Nextflow 25.04:

  • Use eval outputs, topic channels to collect tool versions. Simplify the collection of tool versions, removes lots of boilerplate from processes and workflows. Topic channels are out of preview in 25.04, so they can be used without the feature flag.

  • Use the output block to publish outputs. Publish outputs at workflow level by publishing channels. Use the index file feature to generate the samplesheet. Workflow outputs are still in preview as of 25.04, but I do not expect the syntax to change much at this point.

It should accept the same parameters and produce the exact same outputs as before.

@bentsherman bentsherman requested a review from maxulysse May 14, 2025 20:14
@bentsherman bentsherman mentioned this pull request May 14, 2025
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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: 3.0.2.
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.

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github-actions bot commented May 14, 2025 •
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nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit ddcab5d

+| ✅ 165 tests passed       |+
#| ❔  15 tests were ignored |#

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-fetchngs_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-fetchngs_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-fetchngs_logo_dark.png
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-05-14 20:16:23

This was referenced May 15, 2025
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@edmundmiller edmundmiller added this to the 1.13.0 milestone May 19, 2025
@bentsherman bentsherman mentioned this pull request May 22, 2025
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This was referenced Jun 2, 2025
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@bentsherman bentsherman mentioned this pull request Jun 9, 2025
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@maxulysse maxulysse Awaiting requested review from maxulysse

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