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Add nf-test sharding CI

Open edmundmiller opened this issue 1 year ago • 7 comments

  • ci: Copy over from methylseq
  • ci: Move Sarek specific settings to ci
  • ci: tap => xml

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>).
  • [ ] 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).

edmundmiller avatar Oct 01 '24 19:10 edmundmiller

nf-core pipelines lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit f3b96aa

+| ✅ 215 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

:grey_question: Tests ignored:

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-28 10:13:18

github-actions[bot] avatar Oct 01 '24 19:10 github-actions[bot]

I guess now you'd have a couple of merge conflicts

maxulysse avatar Oct 03 '24 20:10 maxulysse

How to exclude the tags you moved in nf-test-tags.yml?

maxulysse avatar Oct 04 '24 09:10 maxulysse

How to exclude the tags you moved in nf-test-tags.yml?

That's a tough one. I've got https://github.com/askimed/nf-test/issues/260 which we could add to the conda runs.

We could add a conda_pass to everything that works, but that sounds painful. I wonder if we could add a conditional assert if the the profile is conda in the test itself?

Anything that just fails no matter the container abstraction, just mark it as failing with a note that it shouldn't be failing, but ironing out every test is a daunting task that we should handle in a separate PR.

edmundmiller avatar Oct 04 '24 14:10 edmundmiller

merged in https://github.com/nf-core/sarek/pull/1678 Looking good

maxulysse avatar Oct 08 '24 10:10 maxulysse

Synced with dev to include TEMPLATE merge

maxulysse avatar Oct 11 '24 07:10 maxulysse

the last 2 failing tests are fixed in https://github.com/nf-core/sarek/pull/1678

maxulysse avatar Oct 11 '24 07:10 maxulysse