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Forgot to add test_all to nextflow.config #98

Merged
merged 3 commits into from
Oct 17, 2023
Merged

Forgot to add test_all to nextflow.config #98

merged 3 commits into from
Oct 17, 2023

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tillenglert
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@tillenglert tillenglert commented Oct 16, 2023 •
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I forgot to add test_all to the nextflow.config in the last PR for CI tests. and also removed 2 tests (test_bins and test_tiny)

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/metapep 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).

@tillenglert tillenglert marked this pull request as ready for review October 16, 2023 12:51
@tillenglert tillenglert requested a review from skrakau October 16, 2023 12:51
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github-actions bot commented Oct 16, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 07b5974

+| ✅ 151 tests passed       |+
!| ❗   9 tests had warnings |!
-| ❌   5 tests failed       |-

❌ Test failures:

  • files_unchanged - CODE_OF_CONDUCT.md does not match the template
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-16 12:56:29

skrakau
skrakau approved these changes Oct 16, 2023
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LGTM!

@tillenglert tillenglert merged commit 8bea247 into nf-core:dev Oct 17, 2023
@tillenglert tillenglert deleted the bugfix/CI_test_all branch March 11, 2024 05:48
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@skrakau skrakau skrakau approved these changes

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@tillenglert @skrakau