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Add ANCOMBC #753

Merged
merged 21 commits into from
Jun 25, 2024
Merged

Add ANCOMBC #753

merged 21 commits into from
Jun 25, 2024

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d4straub
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@d4straub d4straub commented Jun 21, 2024 •
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We have ANCOM for differential abundance analysis via QIIME2 in the pipeline. However, that is not optimal because rather outdated, allows only pairwise comparisons, and doesnt actually use p-values (valued by many). So I added ANCOM-BC via QIIME2 besides ANCOM, including visualisation of the output. I also made both, ANCOM and ANCOM-BC opt-in choices rather than default, because of the long run time.

Addresses #731

Still to do:

  • test whether combined columns / interactions work with --ancombc_formula
  • add section to output docu
  • add citations to CITATIONS.md
  • add section to pipeline summary report
  • short paragraph in the usage docu
  • update pipeline figure

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/ampliseq 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).

@d4straub d4straub added this to the 2.10.0 milestone Jun 21, 2024
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github-actions bot commented Jun 21, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3932f8e

+| ✅ 285 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-25 08:02:56

@d4straub d4straub marked this pull request as ready for review June 24, 2024 07:51
erikrikarddaniel
erikrikarddaniel approved these changes Jun 24, 2024
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Looks good, but I have question. Will approve anyway and leave deciding for you.

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@d4straub
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Thanks!

@d4straub d4straub merged commit 19f49e6 into nf-core:dev Jun 25, 2024
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@d4straub d4straub deleted the add-ancombc branch June 25, 2024 08:32
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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