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Add an nf-test CI #1288

Merged
merged 14 commits into from
Oct 17, 2023
Merged

Add an nf-test CI #1288

merged 14 commits into from
Oct 17, 2023

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adamrtalbot
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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 (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).

@adamrtalbot
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FYI "Check for changes" will never happen because it has been split in two:

  • Check for changes (pytest)
  • Check for changes (nf-test)

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github-actions bot commented Oct 16, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9f7d685

+| ✅ 144 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • 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: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-17 09:56:52

adamrtalbot
adamrtalbot commented Oct 16, 2023
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maxulysse
maxulysse reviewed Oct 17, 2023
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do we need this file?

@maxulysse maxulysse merged commit 969993e into nf-core:dev Oct 17, 2023
24 of 41 checks passed
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@adamrtalbot @maxulysse