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Revert multiqc workaround #1359

Merged
merged 4 commits into from
Aug 22, 2024
Merged

Revert multiqc workaround #1359

merged 4 commits into from
Aug 22, 2024

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pinin4fjords
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There was unexpectedly a patch release for multiqc with a fix included, so we can revert what we did in #1357.

(multiqc installed off the PR branch pending singularity, will fix the modules.json when that resolves)

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/rnaseq 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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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 @pinin4fjords,

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

@pinin4fjords pinin4fjords changed the base branch from master to dev August 21, 2024 16:19
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github-actions bot commented Aug 21, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 52de9f6

+| ✅ 173 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-22 08:40:39

@pinin4fjords pinin4fjords marked this pull request as draft August 21, 2024 16:22
maxulysse
maxulysse approved these changes Aug 21, 2024
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ok once properly updated

@pinin4fjords pinin4fjords marked this pull request as ready for review August 22, 2024 08:39
@pinin4fjords pinin4fjords merged commit f6af6d9 into dev Aug 22, 2024
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@maxulysse maxulysse maxulysse approved these changes

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@pinin4fjords @maxulysse