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Important! Template update for nf-core/tools v2.13 #171

Merged
merged 5 commits into from
Feb 27, 2024
Merged

Important! Template update for nf-core/tools v2.13 #171

merged 5 commits into from
Feb 27, 2024

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nf-core-bot
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Version 2.13 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-2.13 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 v2.13 release page.

@mashehu
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mashehu commented Feb 23, 2024

did you want to remove the dump_software module? if so, best to use the nf-core modules remove command

@subwaystation
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I just wanted to make this PR work. It became a mess.

@subwaystation
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Closing this in favor of a new one for a cleaner start.

@subwaystation subwaystation reopened this Feb 23, 2024
@subwaystation
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I just want to remove the last commit LUL. So hard.

@subwaystation subwaystation force-pushed the nf-core-template-merge-2.13 branch from 6e4b434 to ccb1668 Compare February 23, 2024 15:20
@subwaystation
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Fantastic, now I can start from scratch. AGAIN.

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github-actions bot commented Feb 27, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c038675

+| ✅ 187 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • 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!
  • schema_description - No description provided in schema for parameter: wfmash_hg_filter_ani_diff

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-pangenome_logo_light.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-27 10:02:12

Zethson
Zethson approved these changes Feb 27, 2024
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🌚

@subwaystation subwaystation merged commit e1f188b into dev Feb 27, 2024
15 checks passed
@subwaystation subwaystation deleted the nf-core-template-merge-2.13 branch February 27, 2024 10:26
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@Zethson Zethson Zethson approved these changes

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@nf-core-bot @mashehu @subwaystation @Zethson