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Update test profile#692

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maxulysse merged 6 commits intonf-core:devfrom
maxulysse:dev_test_profile
Sep 1, 2022
Merged

Update test profile#692
maxulysse merged 6 commits intonf-core:devfrom
maxulysse:dev_test_profile

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@maxulysse maxulysse commented Jul 27, 2022

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 maxulysse changed the base branch from master to dev July 27, 2022 14:27
@nf-core nf-core deleted a comment from github-actions bot Jul 27, 2022
@maxulysse maxulysse changed the title Dev test profile Update test profile Jul 27, 2022
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github-actions bot commented Jul 27, 2022 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit af01590

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

❌ 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

❔ 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

✅ Tests passed:

Run details

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

@nf-core nf-core deleted a comment from github-actions bot Jul 27, 2022
@maxulysse maxulysse marked this pull request as draft July 27, 2022 14:55
@maxulysse maxulysse marked this pull request as ready for review August 24, 2022 08:51
FriederikeHanssen
FriederikeHanssen reviewed Aug 24, 2022
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There is a doc section about what to expect from the tests, that would also need updating.

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maxulysse commented Sep 1, 2022

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.

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FriederikeHanssen commented Sep 1, 2022

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)

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maxulysse commented Sep 1, 2022

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

@maxulysse maxulysse merged commit 2231dcd into nf-core:dev Sep 1, 2022
@maxulysse maxulysse deleted the dev_test_profile branch September 1, 2022 09:46
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