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Don't use contrasts directly from the input channel #175

Merged
merged 1 commit into from
Oct 18, 2023
Merged

Don't use contrasts directly from the input channel #175

merged 1 commit into from
Oct 18, 2023

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pinin4fjords
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Tiny fix to use contrasts from the validator process rather than directly from the input file. That allows us to buffer any assumptions on contrasts file structure via that process.

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).

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github-actions bot commented Oct 18, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 57f32e5

+| ✅ 159 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowDifferentialabundance.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-18 08:01:29

@pinin4fjords
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Thanks @WackerO !

@pinin4fjords pinin4fjords merged commit f2431bb into dev Oct 18, 2023
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@pinin4fjords pinin4fjords deleted the fix_contrasts_usage branch October 18, 2023 08:15
@pinin4fjords pinin4fjords mentioned this pull request Oct 18, 2023
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@pinin4fjords pinin4fjords linked an issue Oct 18, 2023 that may be closed by this pull request
Documentation does not fit pipeline behaviour. #156
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@pinin4fjords pinin4fjords mentioned this pull request Oct 18, 2023
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@WackerO WackerO WackerO approved these changes

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Hackathon: November 2023
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Documentation does not fit pipeline behaviour.
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@pinin4fjords @WackerO