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fix(tests): remove md5sum for all mosdepth tests + update dependency for these tests #1499

Merged
merged 2 commits into from
May 4, 2024
Merged

fix(tests): remove md5sum for all mosdepth tests + update dependency for these tests #1499

merged 2 commits into from
May 4, 2024

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maxulysse
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Should fix all failing tests in the release PR

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).

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github-actions bot commented May 3, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5f2dc64

+| ✅ 180 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.4.2
  • 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_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSarek.groovy
  • 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 or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-04 11:05:26

maxulysse
maxulysse commented May 4, 2024
View reviewed changes
tests/test_gatk4spark.yml Outdated Show resolved Hide resolved
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asp8200 commented May 4, 2024

Were those tests failing because of my update of mosdepth? If so, why didn't those tests failing on my PR? Weren't those tests triggered on my PR?

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asp8200 commented May 4, 2024

Were those tests failing because of my update of mosdepth? If so, why didn't those tests failing on my PR? Weren't those tests triggered on my PR?

Ah, I see that some dependencies to mosdepth were missing in tests/config/pytesttags.yml. Thanks for fixing that 👏

@maxulysse maxulysse merged commit 017d1ee into nf-core:dev May 4, 2024
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@asp8200 asp8200 asp8200 approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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@maxulysse @asp8200