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Merged
maxulysse merged 2 commits into from
Aug 15, 2025
Merged

Exclude star rsem pca from snaps #1594

maxulysse merged 2 commits into from
Aug 15, 2025

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@pinin4fjords pinin4fjords commented Aug 15, 2025

We already excluded the salmon-driven PCA stats for instability, we need to do the same for RSEM. Results have drifted in new conda builds, invalidating the tests in #1593.

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  • 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 pipelines lint).
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  • Usage Documentation in docs/usage.md is updated.
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github-actions bot commented Aug 15, 2025

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 15, 2025 13:15
@pinin4fjords pinin4fjords requested a review from maxulysse August 15, 2025 13:17
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github-actions bot commented Aug 15, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a0894b4

+| ✅ 289 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 3.20.0
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-08-15 13:20:10

@pinin4fjords pinin4fjords enabled auto-merge August 15, 2025 13:20
@maxulysse maxulysse disabled auto-merge August 15, 2025 13:24
@maxulysse maxulysse merged commit 18fd3e8 into dev Aug 15, 2025
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@pinin4fjords pinin4fjords mentioned this pull request Aug 15, 2025
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