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Remove stub run in download_pipeline.yml #471

Merged
merged 4 commits into from
Apr 16, 2024
Merged

Remove stub run in download_pipeline.yml #471

merged 4 commits into from
Apr 16, 2024

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LilyAnderssonLee
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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/taxprofiler 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 Apr 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8fe3968

+| ✅ 192 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.1.6
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-16 07:28:12

@Midnighter
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Isn't it supposed to be dev? Just had a brief read through Slack, so I'm likely wrong.

@LilyAnderssonLee
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Aha, I misunderstood it then. So I should change it to like this?
nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< dev) -stub -profile test,singularity --outdir ./results

MatthiasZepper
MatthiasZepper requested changes Apr 12, 2024
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@MatthiasZepper MatthiasZepper left a comment

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This PR will sadly not change anything with regard to the action. Because you want to merge the changes into the dev branch of your pipeline. So after merging, you change dev.

Whatever change is being made to that Github Action will however not take effect before merged to master.

So the problem is not, that there are still issues with the updated test (after #470 that looks good) but that the version that is run for checking your release PR is the version of the test released with Taxprofiler 1.1.5 in February. Until 1.1.6 is out, whatever changes you and Sofia made since, are disregarded.

So you only have two options: Publish the new release despite the failing test, or patch the master branch first. (That is pushing the modified CI pipeline to master, which may be rejected due to branch protection rules...)

.github/workflows/download_pipeline.yml Show resolved Hide resolved
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@LilyAnderssonLee LilyAnderssonLee changed the title Manually define stub run branch as master Remove stub run in download_pipeline.yml Apr 16, 2024
jfy133
jfy133 reviewed Apr 16, 2024
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LGTM. I guess you could just commetn out the stub version rather than remove it entirely, but same thing for now and I'm sure can fix in a future tmplate merge :)

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jfy133 commented Apr 16, 2024

Ah let's skip it for now

@jfy133 jfy133 self-requested a review April 16, 2024 08:44
@jfy133 jfy133 merged commit e805e26 into nf-core:dev Apr 16, 2024
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@LilyAnderssonLee LilyAnderssonLee deleted the download-pipeline-bug branch June 25, 2024 13:49
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@Midnighter Midnighter Midnighter left review comments

@sofstam sofstam sofstam left review comments

@MatthiasZepper MatthiasZepper MatthiasZepper requested changes

@maxulysse maxulysse maxulysse approved these changes

@jfy133 jfy133 jfy133 approved these changes

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@LilyAnderssonLee @Midnighter @jfy133 @maxulysse @MatthiasZepper @sofstam