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Use nf-core/setup-nf-test action for reusability #316

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Use nf-core/setup-nf-test action for reusability #316

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@adamrtalbot adamrtalbot commented Jul 5, 2024 •
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Replaces custom nf-test setup with setup-nf-test action from nf-core. This should enhance code reusability.

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/fetchngs 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>).
  • 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 Jul 5, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit d96b1bc

+| ✅ 152 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌   5 tests failed       |-

❌ Test failures:

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-05 15:28:26

@adamrtalbot
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Linting!!! :shakefist:

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@maxulysse maxulysse Awaiting requested review from maxulysse

@drpatelh drpatelh Awaiting requested review from drpatelh

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