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Fix deepARG test profile and use more stable deepARG db URL #307

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merged 7 commits into from
Aug 25, 2023
Merged

Fix deepARG test profile and use more stable deepARG db URL #307

merged 7 commits into from
Aug 25, 2023

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jfy133
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@jfy133 jfy133 commented Aug 25, 2023

This stabilises the deepARG tests by using the Zenodo uploaded copy of the database.

Note I added the skiup abricate to the test profile to speed up run time (even if it's fast), I also reduced the number of annotation tools to test, to stop us being throttled by Zenodo if we have lots of parallel downloads of the file

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/funcscan 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).

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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 @jfy133,

It looks like this pull-request is has been made against the nf-core/funcscan 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/funcscan 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!

@jfy133 jfy133 changed the base branch from master to dev August 25, 2023 06:58
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github-actions bot commented Aug 25, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit bc4db0d

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-25 09:14:46

@jfy133 jfy133 requested a review from a team August 25, 2023 07:05
louperelo
louperelo approved these changes Aug 25, 2023
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Looks good. How nice that this test will work now!

jfy133
jfy133 commented Aug 25, 2023
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louperelo
louperelo approved these changes Aug 25, 2023
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Looks good to me

jfy133
jfy133 commented Aug 25, 2023
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Fixing the path

@jfy133 jfy133 merged commit 342b848 into dev Aug 25, 2023
@jfy133 jfy133 deleted the stablish-deeparg branch August 25, 2023 11:11
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@jfy133 @louperelo @jasmezz