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Add design to report #189

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merged 5 commits into from
Nov 22, 2023
Merged

Add design to report #189

merged 5 commits into from
Nov 22, 2023

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WackerO
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@WackerO WackerO commented Nov 8, 2023 •
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This PR adds the design formulas to the contrasts table in the report file as in this example:
SRP254919_design.html.zip

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).

@WackerO WackerO mentioned this pull request Nov 8, 2023
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pinin4fjords
pinin4fjords reviewed Nov 9, 2023
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assets/differentialabundance_report.Rmd Outdated

# If DESeq2 was run instead of Limma, add designs to report
if (params$study_type %in% c('rnaseq')) {
contrasts_to_print[["DESeq2 models"]] <- paste('~ 0 + ', ifelse(contrasts_to_print$Blocking != '', make.names(contrasts_to_print$Blocking), ''), '+ ', make.names(contrasts_to_print$Variable))
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I'm not a fan of this, since it will require careful attention if the DESeq2 module is updated.

If you really want this, suggest you have DESeq2 (and, ideally, Limma) modules output the models in some way, so we can retrieve it here.

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Yeah, I also considered that...Alright, will for now have a look at adding some DESeq2 output

pinin4fjords
pinin4fjords requested changes Nov 9, 2023
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Sorry, I worry about keeping this up to date with module code- reject for now.

@WackerO WackerO marked this pull request as draft November 9, 2023 12:09
@WackerO WackerO marked this pull request as ready for review November 14, 2023 09:23
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github-actions bot commented Nov 21, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 8d5ea35

+| ✅ 160 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-21 15:44:52

@WackerO WackerO requested a review from pinin4fjords November 21, 2023 14:35
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pinin4fjords reviewed Nov 21, 2023
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Looking pretty good- don't forget the changelog, and could you post an example report from this?

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WackerO commented Nov 21, 2023

Here you go: SRP254919.html.zip

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pinin4fjords approved these changes Nov 22, 2023
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Noticing we have the '+ +' we should fix in the d/e modules, but looks good.

@WackerO WackerO merged commit 4587680 into nf-core:dev Nov 22, 2023
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@WackerO WackerO deleted the design branch November 22, 2023 09:20
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@WackerO @pinin4fjords