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Add parameters and random terms for local module DREAM_DIFFERENTIAL #416

Merged
merged 13 commits into from
Jan 7, 2025
Merged

Add parameters and random terms for local module DREAM_DIFFERENTIAL #416

merged 13 commits into from
Jan 7, 2025

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alanmmobbs93
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@alanmmobbs93 alanmmobbs93 commented Dec 31, 2024 •
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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).

Changed

  • Add parameters to control dream(), variancePartition::eBayes(), and variancePartition::topTable() functions within DREAM_DIFFERENTIAL module.
  • Add blocking factors as random effects to the formula.

Fixed

  • Fix bug with when getting blocking factors from the meta array.

Perspectives

  • Greate complex contrasts from yml file.

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Dec 31, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0436b97

+| ✅ 310 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 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!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-01-07 18:15:06

@alanmmobbs93 alanmmobbs93 marked this pull request as ready for review December 31, 2024 23:15
nschcolnicov
nschcolnicov reviewed Jan 2, 2025
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modules/local/dream/differential/resources/usr/bin/dream_de.R
################################################
################################################
## PARSE PARAMETERS FROM NEXTFLOW ##
################################################
################################################
library(optparse)
cat("Parsing arguments\n")

# Define the full list of options
option_list <- list(
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These three options seem to be missing:
stdev.coef.lim
winsor.tail.p
p.value

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@alanmmobbs93 alanmmobbs93 Jan 6, 2025 •
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@nschcolnicov Thanks! They are, but with the dots replaced by underscores. Did you find the parameters as you wrote them somewhere else?

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Ahh I see, I saw them written that way in the modules.config:
i.e:

differentialabundance/conf/modules.config

Line 288 in d760b85

"--p.value ${params.limma_p_value}",

Let me know if I'm making a mistake

nschcolnicov
nschcolnicov requested changes Jan 2, 2025
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Please update the docs/usage.md and docs/output.md

atrigila
atrigila reviewed Jan 6, 2025
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modules/local/dream/differential/main.nf Show resolved Hide resolved
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@alanmmobbs93 alanmmobbs93 requested a review from atrigila January 7, 2025 13:51
atrigila
atrigila approved these changes Jan 7, 2025
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Makes sense to me from the module's perspective but I am not 100% familiar with the pipeline and method, so we can wait for Nico's feedback as well :)

nschcolnicov
nschcolnicov approved these changes Jan 7, 2025
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Thanks for addressing the comments!

@alanmmobbs93 alanmmobbs93 merged commit 98f5596 into nf-core:dev_tmp Jan 7, 2025
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@nschcolnicov nschcolnicov nschcolnicov approved these changes

@atrigila atrigila atrigila approved these changes

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@alanmmobbs93 @nf-core-bot @atrigila @nschcolnicov