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Important! Template update for nf-core/tools v2.14.1 #1297

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merged 4 commits into from May 13, 2024

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Version 2.14.1 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-2.14.1 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 v2.14.1 release page.

Comment on lines +317 to +318
- `wave`
- A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
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@drpatelh drpatelh May 13, 2024

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@maxulysse we need to update this in the template if we rename the profile as in #1291

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Indeed, I was thinking the exact same

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Are we 100% sure with the name?

Comment on lines +317 to +318
- `wave`
- A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
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Suggested change
- `wave`
- A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
- `seqera_containers`
- A generic configuration profile to enable [Wave](https://seqera.io/wave/) and to build and pull from the Seqera containers repository. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).

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If this originates in the template we should update it there first.

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Yep, we can update it in #1291 first so everything is updated as an example, and then push to the template. Think we have some agreement but will allow time for more discussions.

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@drpatelh drpatelh May 13, 2024

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@maxulysse when we have merged this PR can you pull in the changes from dev and make this update in #1291 please?

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Done 8b0e4a5

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github-actions bot commented May 13, 2024

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 27b1503

+| ✅ 171 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-13 11:14:37

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@maxulysse maxulysse left a comment

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Good for me, just need to be sure about the name for the new profile, and I can propagate that to the TEMPLATE

@drpatelh drpatelh merged commit 431edb0 into dev May 13, 2024
185 checks passed
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4 participants