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Overhaul tximport.r, output length tables #1123

Merged
merged 10 commits into from
Nov 21, 2023
Merged

Overhaul tximport.r, output length tables #1123

merged 10 commits into from
Nov 21, 2023

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pinin4fjords
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@pinin4fjords pinin4fjords commented Nov 20, 2023 •
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This PR overhauls the scrappy tximport script, and adds transcript length output so that e.g. differentialabundance can do robust differential analysis from tximport 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>).
  • 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).

@pinin4fjords pinin4fjords marked this pull request as draft November 20, 2023 12:14
@pinin4fjords pinin4fjords changed the base branch from master to dev November 20, 2023 12:14
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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!

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github-actions bot commented Nov 20, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 56edb1c

+| ✅ 144 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 3.13.1
  • 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 WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-21 09:19:15

@pinin4fjords pinin4fjords changed the title [WIP] overhaul tximport.r [WIP] overhaul tximport.r, output length tables Nov 20, 2023
@pinin4fjords pinin4fjords changed the title [WIP] overhaul tximport.r, output length tables Overhaul tximport.r, output length tables Nov 20, 2023
@pinin4fjords pinin4fjords marked this pull request as ready for review November 20, 2023 17:39
maxulysse
maxulysse requested changes Nov 21, 2023
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CHANGELOG?

maxulysse
maxulysse reviewed Nov 21, 2023
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@pinin4fjords
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Thanks @maxulysse !

@pinin4fjords pinin4fjords merged commit 79443ec into dev Nov 21, 2023
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@pinin4fjords pinin4fjords deleted the improve_tximport branch November 21, 2023 09:25
@olgabot olgabot mentioned this pull request Jun 18, 2024
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@maxulysse maxulysse maxulysse approved these changes

@drpatelh drpatelh Awaiting requested review from drpatelh

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@pinin4fjords @maxulysse