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Split ch_tools into subworkflow relevant subchannels #308

Merged
merged 8 commits into from
Oct 23, 2024
Merged

Split ch_tools into subworkflow relevant subchannels #308

merged 8 commits into from
Oct 23, 2024

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bjlang
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@bjlang bjlang commented Oct 22, 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).

@bjlang
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bjlang commented Oct 22, 2024

@nf-core-bot fix linting

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github-actions bot commented Oct 22, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4075a80

+| ✅ 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 2024-10-23 12:35:05

suzannejin
suzannejin reviewed Oct 23, 2024
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conf/test_experimental.config Outdated
@@ -29,7 +29,8 @@ params {
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv'
matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv'
contrasts = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv'
pathway = "propd,propd_grea,propr,cor"
tools = "$projectDir/assets/tools_samplesheet.csv"
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tools is now declared inside nextflow.config with default value assets/tools_samplesheet.csv, so you don't need it here

suzannejin
suzannejin reviewed Oct 23, 2024
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workflows/differentialabundance.nf
def correlation_map = it[0].subMap(["cor_method","args_cor"])
def enrichment_map = it[0].subMap(["enr_method","args_enr"])
[ pathway_name, differential_map, correlation_map, enrichment_map ]
}.unique()
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this is super clean! I like it!

suzannejin
suzannejin reviewed Oct 23, 2024
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assets/tools_samplesheet.csv
@@ -5,3 +5,4 @@ pcorbshrink,,,propr,--metric pcor.bshrink,,
propr,,,propr,--metric rho,,
cor,,,propr,--metric cor,,
propd_grea,propd,,,,grea,
deseq2,deseq2,,,,gsea,
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deseq2 does not do anything yet here no?

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No, just a placeholder for how it would look like. And with your new additions it would become functional, right?

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yes, with the new additions it would be good!

suzannejin
suzannejin reviewed Oct 23, 2024
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subworkflows/local/enrichment/main.nf
}
.branch {
grea: it[0]["enr_method"] == "grea"
gsea: it[0]["enr_method"] == "gsea"
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gsea dont use ch_adjacency as input.
So we can maybe just branch ch_tools into grea and gsea at the beginning, and use ch_tools.grea in the GREA section to combine it with ch_adjacency

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Ok, yes, that sounds good to me. But I'd would change it then when we include gsea.

@suzannejin
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Thank you @bjlang overall it looks good to me!
I think this improves the encapsulation of each subworkflow.
The only thing is that they are still pathway dependent instead of specific to each diff/corr/enr method right? In this way, each subworkflow still have to somehow understand what a 'pathway' is.
And are the processes (ie. diff and corr) with different pathway name but same args/input still repeating the computation maybe?

@bjlang bjlang marked this pull request as ready for review October 23, 2024 13:51
@bjlang bjlang merged commit a594ebf into nf-core:dev-ratio Oct 23, 2024
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@bjlang @suzannejin