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Change name to nf-core/spatialvi #77

Merged
merged 2 commits into from
Apr 18, 2024
Merged

Change name to nf-core/spatialvi #77

merged 2 commits into from
Apr 18, 2024

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fasterius
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@fasterius fasterius commented Apr 17, 2024 •
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As per discussions in the nf-core community, this commit changes the name of the pipeline from nf-core/spatialtranscriptomics to nf-core/spatialvi.

Related PR for test data is at nf-core/test-datasets#1185. (Now merged.)

PR checklist

  • This comment contains a description of changes (with reason).
  • If necessary, also make a PR on the nf-core/spatialtranscriptomics branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint). (logo linting partially fails, but as per Slack discussions we should ignore this for now and update the logos once the name change is complete)
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).

@fasterius
Change name to nf-core/spatialvi
5c033e3 
As per discussions in the nf-core community, this commit changes the
name of the pipeline from `nf-core/spatialtranscriptomics` to
`nf-core/spatialvi`. The old name is descriptive in regards to what it
does, but not specific enough, as it analyses 10X Visium data
exclusively. It was determined that spatial nf-core pipelines should be
named according to the `spatialXX` pattern; another pipeline named
`nf-core/spatialxe` for Xenium data already exists.
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github-actions bot commented Apr 17, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit da2b332

+| ✅ 173 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   3 tests had warnings |!
-| ❌   2 tests failed       |-

❌ Test failures:

  • files_unchanged - docs/images/nf-core-spatialvi_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-spatialvi_logo_dark.png does not match the template

❗ Test warnings:

  • 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 citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-18 09:43:53

@fasterius fasterius mentioned this pull request Apr 17, 2024
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fasterius commented Apr 18, 2024 •
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Okay, everything that can succeed has succeeded! The linting fails and can be ignored per Slack discussions, and the one CI that fails fails for a known reason that can be ignored for now (the solution is ready and waiting for the next MultiQC release).

@fasterius fasterius marked this pull request as ready for review April 18, 2024 09:37
@fasterius fasterius merged commit 0d9fc74 into dev Apr 18, 2024
4 of 6 checks passed
@fasterius fasterius deleted the namechange branch April 18, 2024 09:59
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@maxulysse maxulysse maxulysse approved these changes

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@fasterius @maxulysse @cavenel