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318 update for tes compliance #320

Merged
merged 17 commits into from
Oct 15, 2024
Merged

318 update for tes compliance #320

merged 17 commits into from
Oct 15, 2024

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vsmalladi
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@vsmalladi vsmalladi commented Sep 16, 2024 •
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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/fetchngs 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).

@github-actions GitHub Actions
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @vsmalladi,

It looks like this pull-request is has been made against the nf-core/fetchngs master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/fetchngs dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@github-actions GitHub Actions
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github-actions bot commented Sep 16, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d0e3777

+| ✅ 167 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-15 15:09:53

@vsmalladi vsmalladi changed the base branch from master to dev September 16, 2024 03:57
maxulysse
maxulysse reviewed Oct 14, 2024
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Linting is failing, but it's ok, I'll finish working up on TEMPLATE sync and then merge this one.
sorry for the delay @vsmalladi

@vsmalladi
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Great thanks @maxulysse

@maxulysse
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That looks good to me, but I'm asking an extra set of eyes for safety because of the updates in all the tests

JoseEspinosa
JoseEspinosa approved these changes Oct 15, 2024
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LGTM! Just a small formatting suggestion

modules/local/multiqc_mappings_config/main.nf Outdated Show resolved Hide resolved
@maxulysse maxulysse enabled auto-merge October 15, 2024 15:08
@vsmalladi
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Awesome. I think I can update the rest for tea compliance as well

@maxulysse maxulysse merged commit 7544cb9 into dev Oct 15, 2024
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@maxulysse maxulysse deleted the 318-update-for-tes-compliance branch November 11, 2024 17:31
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@maxulysse maxulysse maxulysse left review comments

@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@adamrtalbot adamrtalbot Awaiting requested review from adamrtalbot

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3 participants
@vsmalladi @maxulysse @JoseEspinosa