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Add taxpasta taxdir check #393

Merged
merged 4 commits into from
Oct 7, 2023
Merged

Add taxpasta taxdir check #393

merged 4 commits into from
Oct 7, 2023

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jfy133
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@jfy133 jfy133 commented Oct 6, 2023

closes #390

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>).
  • 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 Oct 6, 2023

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/taxprofiler 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/taxprofiler 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 October 6, 2023 12:11
jfy133
jfy133 commented Oct 6, 2023
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github-actions bot commented Oct 6, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0b54be1

+| ✅ 158 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.1.1
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • 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 2.10
  • Run at 2023-10-07 15:07:49

Midnighter
Midnighter approved these changes Oct 6, 2023
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I didn't check why the tests are failing, the code looks good to me.

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jfy133 commented Oct 7, 2023

Final failures are problem with GHA. running locally fine 👍

@jfy133 jfy133 merged commit 4c2014e into dev Oct 7, 2023
23 of 26 checks passed
@jfy133 jfy133 deleted the add-taxpasta-taxdir-check branch October 7, 2023 17:52
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@Midnighter Midnighter Midnighter approved these changes

@LilyAnderssonLee LilyAnderssonLee Awaiting requested review from LilyAnderssonLee

@sofstam sofstam Awaiting requested review from sofstam

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