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Fix up sample exclusion options #132

Merged
merged 5 commits into from
Jul 25, 2023
Merged

Fix up sample exclusion options #132

merged 5 commits into from
Jul 25, 2023

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pinin4fjords
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@pinin4fjords pinin4fjords commented May 26, 2023 •
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Closes #133

Basically we can no longer assume that the first differential run will produce a normalised matrix we can use globally. So we run the 'differential' module once purely for normalisation purposes. Eventually we should have a normalisation module I guess, but this will work fine for now.

The module-level changes have already been reviewed in nf-core/modules#3664.

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 marked this pull request as draft May 26, 2023 12:11
@pinin4fjords pinin4fjords added the WIP This issue is already being worked on label May 26, 2023
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github-actions bot commented May 26, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 8a91954

+| ✅ 158 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-25 10:06:48

@pinin4fjords pinin4fjords linked an issue May 26, 2023 that may be closed by this pull request
Sample exclusion options fail due to contrast-wise normalisation #133
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@pinin4fjords pinin4fjords mentioned this pull request Jul 23, 2023
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@pinin4fjords pinin4fjords removed the WIP This issue is already being worked on label Jul 25, 2023
@pinin4fjords pinin4fjords marked this pull request as ready for review July 25, 2023 09:33
WackerO
WackerO approved these changes Jul 25, 2023
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LGTM

@pinin4fjords pinin4fjords merged commit 28f0ae0 into nf-core:dev Jul 25, 2023
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@pinin4fjords pinin4fjords deleted the fix_excluded_samples branch July 25, 2023 10:15
@pinin4fjords pinin4fjords added this to the 1.3.0 milestone Oct 10, 2023
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Sample exclusion options fail due to contrast-wise normalisation
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