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322 add module deseq2 #335

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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).

@roskamsh roskamsh requested a review from WackerO October 30, 2024 11:25
@roskamsh roskamsh linked an issue Oct 30, 2024 that may be closed by this pull request
add module DESEQ2 #322
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github-actions bot commented Oct 30, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a885116

+| ✅ 317 tests passed       |+
#| ❔   7 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 2024-10-30 14:23:53

WackerO
WackerO reviewed Oct 30, 2024
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subworkflows/local/differential/main.nf
}
.set { ch_deseq2 }

// do we need this process DESEQ2_NORM?
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Yes, we do 🙂

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WackerO commented Oct 30, 2024 •
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Hey @roskamsh, thanks for taking over this issue! Nice work, just a couple of small changes.

@suzannejin I just had a quick look at the output and was wondering if you know why the DESeq2 result tables differ slightly in the test_experimental profile when compared to the test profile:

test:

gene_id	baseMean	log2FoldChange	lfcSE	pvalue	padj
ENSMUSG00000023978	309.50335903	5.015358	2.7289078	NA	NA
ENSMUSG00000030324	1881.77922741	0.9717132	2.0668858	NA	NA
ENSMUSG00000031450	195.24652216	0.8356462	1.90527993	NA	NA

experimental:

gene_id	baseMean	log2FoldChange	lfcSE	pvalue	padj
ENSMUSG00000023978	308.89789121	5.406014	2.57197697	NA	NA
ENSMUSG00000030324	1763.85049182	1.057522	2.14925341	NA	NA
ENSMUSG00000031450	201.02654536	1.131211	2.19318651	NA	NA

@roskamsh
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Hey @roskamsh, thanks for taking over this issue! Nice work, just a couple of small changes.

@suzannejin I just had a quick look at the output and was wondering if you know why the DESeq2 result tables differ slightly in the test_experimental profile when compared to the test profile:

test:

gene_id	baseMean	log2FoldChange	lfcSE	pvalue	padj
ENSMUSG00000023978	309.50335903	5.015358	2.7289078	NA	NA
ENSMUSG00000030324	1881.77922741	0.9717132	2.0668858	NA	NA
ENSMUSG00000031450	195.24652216	0.8356462	1.90527993	NA	NA

experimental:

gene_id	baseMean	log2FoldChange	lfcSE	pvalue	padj
ENSMUSG00000023978	308.89789121	5.406014	2.57197697	NA	NA
ENSMUSG00000030324	1763.85049182	1.057522	2.14925341	NA	NA
ENSMUSG00000031450	201.02654536	1.131211	2.19318651	NA	NA

Could this be due to the new parameter I added in the test_experimental.config file? When the DESEQ2 process ran as initially specified, this line (https://github.com/nf-core/differentialabundance/blob/dev-ratio/modules/nf-core/deseq2/differential/templates/deseq_de.R#L486) threw an error, saying that nsub was greater that nrow. I went in and replicated the issue myself, and it seems that the input matrix only contained 982 features, whereas the vst_nsub default value was set to 1000. In order to resolve this I had to change the nextflow parameter vst_nsub in the test_experimental.config file. I am not really sure why this wasn't found in the test run itself, if the input data is exactly the same?

Is the input data exactly the same? Even so, this would only really change the *.vst.tsv output and not the *.deseq2.results.tsv output.

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add module DESEQ2
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@roskamsh @WackerO