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[dev-ratio] simplified toolsheet structure, and modified the subworkflows accordingly #293

Merged
merged 9 commits into from
Oct 7, 2024
Merged

[dev-ratio] simplified toolsheet structure, and modified the subworkflows accordingly #293

merged 9 commits into from
Oct 7, 2024

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suzannejin
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Hello! Just restructured the toolsheet into the following three blocks:
1- differential analysis
2- correlation analysis
3- enrichment analysis
Also the subworkflows were modified accordingly to accomodate for the new block structure.

In the coming days I will update the modules from these three blocks as well (maybe first as local modules), and then change the arguments from the toolsheet accordingly.

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 (nf-test test main.nf.test -profile test,docker).
  • 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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github-actions bot commented Oct 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 283385a

+| ✅ 299 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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 2024-10-03 09:59:27

bjlang
bjlang approved these changes Oct 2, 2024
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Since the variable_selection subworkflow and with it the filtervar module aren't used anymore, can they be deleted?
Besides it looks good to me!

@suzannejin
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Since the variable_selection subworkflow and with it the filtervar module aren't used anymore, can they be deleted? Besides it looks good to me!

good point! they are removed now :)

@suzannejin suzannejin merged commit 25ace61 into nf-core:dev-ratio Oct 7, 2024
13 of 14 checks passed
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@bjlang bjlang bjlang approved these changes

@pinin4fjords pinin4fjords Awaiting requested review from pinin4fjords

@WackerO WackerO Awaiting requested review from WackerO

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@suzannejin @bjlang