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Published 20 hours ago • verified publisher icon nf-core

Update test profile

Open maxulysse opened this issue 3 years ago • 1 comments

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).

maxulysse avatar Jul 27 '22 14:07 maxulysse

nf-core lint overall result: Failed :x:

Posted for pipeline commit af01590

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
-| ❌   4 tests failed       |-

:x: Test failures:

  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • actions_ci - '.github/workflows/ci.yml' does not check minimum NF version

:grey_question: Tests ignored:

  • 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

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.5
  • Run at 2022-09-01 09:38:15

github-actions[bot] avatar Jul 27 '22 14:07 github-actions[bot]

There is a doc section about what to expect from the tests, that would also need updating.

We actually don't explain too much there, and I think now with the extensive work that @asp8200 did all the expected files are quite well explained in the yml files. So I feel like we have enough there.

maxulysse avatar Sep 01 '22 09:09 maxulysse

There is a doc section about what to expect from the tests, that would also need updating.

We actually don't explain too much there, and I think now with the extensive work that @asp8200 did all the expected files are quite well explained in the yml files. So I feel like we have enough there.

there is an example output though, that isnot up to date anymore. (otherwise we can also try this new rich click thing, if that works)

FriederikeHanssen avatar Sep 01 '22 09:09 FriederikeHanssen

rich codex should be a separate PR, but I like the idea

maxulysse avatar Sep 01 '22 09:09 maxulysse