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Important! Template update for nf-core/tools v2.9 #290

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merged 9 commits into from Jul 12, 2023

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Version 2.9 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-2.9 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/developers/sync.

For more information about this release of nf-core/tools, please see the v2.9 release page.

@jfy133 jfy133 self-requested a review July 5, 2023 09:11
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github-actions bot commented Jul 5, 2023

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit df5af52

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-12 12:41:58

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jfy133 commented Jul 12, 2023

@nf-core-bot fix linting

@jfy133 jfy133 requested a review from a team July 12, 2023 12:20
CITATIONS.md Outdated Show resolved Hide resolved
@@ -58,6 +66,10 @@

> Ibrahim, A. & Perelo, L. (2023). Darcy220606/AMPcombi. [DOI: 10.5281/zenodo.7639121](https://doi.org/10.5281/zenodo.7639121).

- [hAMRonization](https://github.com/pha4ge/hAMRonization)

> Maguire, F., Fornika, D., Mendes, I., Phelan, J., Underwood, A., Witney, A., pvanheus, Manuele, A., Lee, T., amos, & imendes. (2023). pha4ge/hAMRonization: Zenodo Release. Zenodo. https://doi.org/10.5281/ZENODO.8131134
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GH user handles are fine in references?

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not really but I can't be bothered to look them up...

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Once tests succeed

Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
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jasmezz commented Jul 12, 2023

Anan and Louisa are happy they just said, no extra review needed ;) Go ahead with merging

@jfy133 jfy133 merged commit 8073125 into dev Jul 12, 2023
24 checks passed
@jfy133 jfy133 deleted the nf-core-template-merge-2.9 branch July 12, 2023 13:53
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3 participants