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Nf-test #291

Merged
merged 15 commits into from
Feb 14, 2024
Merged

Nf-test #291

merged 15 commits into from
Feb 14, 2024

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grst
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@grst grst commented Jan 19, 2024

Close #91

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/scrnaseq 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 Jan 19, 2024 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 379f8ad

+| ✅ 175 tests passed       |+
#| ❔   2 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-14 08:26:23

@grst grst requested a review from sateeshperi January 19, 2024 11:51
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grst commented Jan 19, 2024 •
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Thanks @fmalmeida, I don't see any major issue... Could probably add more/all output files to the snapshot.

Asking for additional review by @sateeshperi who has worked more with nf-test afaik

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Cool. I will then first work in prototyping the tests for the other aligners following the same structure, and in the end, based on review and all we can check if we add or remove some files.

😄

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Hi @grst ,
I have added the nf-test run for the main aligners, alevin, star, cellranger and kallisto.
Thus, what is required now is to change the github actions to run them instead of pytests and to have a proper review discussion over the testings.

@grst grst mentioned this pull request Feb 13, 2024
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grst
grst commented Feb 13, 2024
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Really cool, thanks!
I think you could steal the CI part from e.g. fetchngs. Or maybe someone in the nf-test channel on slack has better advice.

I'm happy to merge this soon, this'll add a lot of value!

tests/main_pipeline_alevin.test Outdated Show resolved Hide resolved
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Hi @grst ,
Have addressed your comment and also changed the ci.yml to use nf-test. I think it is working.

@fmalmeida fmalmeida marked this pull request as ready for review February 13, 2024 11:41
grst
grst commented Feb 13, 2024
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lol, I can't approve because I opened the PR but didn't make a single commit 😅

LGTM though - you can probably approve yourself :D I also asked for another review in the nf-core slack.

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Let's see if someone else reviews it then. If not, I can approve tomorrow.

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fmalmeida approved these changes Feb 14, 2024
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Since all was resolved, I am approving it.

@fmalmeida fmalmeida merged commit 7c8989f into dev Feb 14, 2024
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@fmalmeida fmalmeida deleted the 91-implement-tests-with-nf-test branch February 14, 2024 08:37
@fmalmeida fmalmeida linked an issue Feb 14, 2024 that may be closed by this pull request
Implement tests with nf-test #91
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@fmalmeida fmalmeida mentioned this pull request Feb 14, 2024
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@fmalmeida fmalmeida fmalmeida approved these changes

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Implement tests with nf-test
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