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Transcript lengths for DESeq2 #203

Merged
merged 9 commits into from
Nov 22, 2023
Merged

Transcript lengths for DESeq2 #203

merged 9 commits into from
Nov 22, 2023

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pinin4fjords
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This PR adds a much demanded feature- usage of transcript length matrices from tximport when using the outputs of the nf-core rna-seq workflow.

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/differentialabundance 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 changed the title Transcript lengths Transcript lengths for DESeq2 Nov 22, 2023
@pinin4fjords
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@nf-core-bot fix linting

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github-actions bot commented Nov 22, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 9bf5396

+| ✅ 160 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-22 19:39:10

@pinin4fjords pinin4fjords marked this pull request as draft November 22, 2023 17:12
maxulysse
maxulysse approved these changes Nov 22, 2023
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@pinin4fjords
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Thanks @maxulysse !

@pinin4fjords pinin4fjords marked this pull request as ready for review November 22, 2023 19:36
@pinin4fjords pinin4fjords merged commit 0b9aeeb into dev Nov 22, 2023
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@pinin4fjords pinin4fjords deleted the transcript_lengths branch November 22, 2023 22:20
@olgabot olgabot mentioned this pull request Jun 18, 2024
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@maxulysse maxulysse maxulysse approved these changes

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