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Anaconda purge (1.2.3) #156

Merged
merged 7 commits into from
Dec 5, 2024
Merged

Anaconda purge (1.2.3) #156

merged 7 commits into from
Dec 5, 2024

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tkchafin
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@tkchafin tkchafin commented Dec 2, 2024

nf-core module updates

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Dec 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit da38725

+| ✅ 132 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File does not exist: assets/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genomenote/genomenote/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-12-05 16:04:29

@tkchafin tkchafin changed the title 1.2.3 Anaconda purge (1.2.3) Dec 2, 2024
@tkchafin tkchafin requested review from muffato and BethYates December 2, 2024 18:03
@BethYates
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Do we know why the tests are failing?

@muffato
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muffato commented Dec 5, 2024

Do we know why the tests are failing?

Nextflow have released a new version that refuses to run on older Java, but that's the default version used on GitHub CI ...
Apparently, switching to setup-nextflow@v2 may fix it.

@tkchafin tkchafin merged commit 61c56e4 into sanger-tol:1.2.3 Dec 5, 2024
4 of 6 checks passed
@tkchafin tkchafin deleted the 1.2.3 branch December 5, 2024 20:59
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@BethYates BethYates BethYates approved these changes

@muffato muffato Awaiting requested review from muffato

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@tkchafin @BethYates @muffato