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Remove redundant gene TPM outputs #1304

Merged
merged 3 commits into from
May 29, 2024
Merged

Remove redundant gene TPM outputs #1304

merged 3 commits into from
May 29, 2024

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pinin4fjords
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In resolution of #847, and effective reversion of #1302, remove redundant TPM outputs.

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 May 28, 2024 17:04
@pinin4fjords pinin4fjords changed the title No extra tpms Remove redundant gene TPM outputs May 28, 2024
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github-actions bot commented May 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2a86507

+| ✅ 171 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 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 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-28 17:10:03

@pinin4fjords
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Thanks @FriederikeHanssen !

@pinin4fjords pinin4fjords merged commit 21095f3 into dev May 29, 2024
185 checks passed
@pinin4fjords pinin4fjords deleted the no_extra_tpms branch May 29, 2024 09:35
@pinin4fjords pinin4fjords mentioned this pull request May 29, 2024
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@pinin4fjords @FriederikeHanssen