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FIX: drop snapshot from Deepvariant tests #1597

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maxulysse merged 1 commit into from
Jul 22, 2024
Merged

FIX: drop snapshot from Deepvariant tests #1597

maxulysse merged 1 commit into from
Jul 22, 2024

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@maxulysse
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@maxulysse maxulysse commented Jul 16, 2024

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
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test tests/ --verbose --profile +docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@maxulysse maxulysse mentioned this pull request Jul 16, 2024
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github-actions bot commented Jul 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fa9961d

+| ✅ 199 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.4.3
  • 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:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-16 15:33:55

@FriederikeHanssen
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FriederikeHanssen commented Jul 17, 2024

All these dropped snapshots worry me a bit since they have worked before. And just because it is pytest it should still work. Any idea what is going on?

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maxulysse commented Jul 17, 2024

I'm guessing the bcftools update from 1.18 to 1.20, we probably where not capturing all the dependent modules from this change.

@maxulysse maxulysse merged commit 9f11b67 into nf-core:dev Jul 22, 2024
@maxulysse maxulysse deleted the fix_old_pytests_ii branch July 22, 2024 13:34
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