update subworkflows for differential and functional enrichment analysis by suzannejin · Pull Request #11024 · nf-core/modules

suzannejin · 2026-03-23T18:59:36Z

Update subworkflows for differential and functional enrichment analysis.
This update is needed for the workflow output migration here

PR checklist

Closes #XXX

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Pull request overview

Updates nf-core subworkflows used by differential abundance + functional enrichment pipelines to align emitted outputs with an upcoming output migration in nf-core/differentialabundance.

Changes:

Refactors differential_functional_enrichment GSEA wiring (CHIP handling + input reshaping) and adds new artifact output channels for gprofiler2 and GSEA.
Adds new plots and other output channels to abundance_differential_filter and updates workflow wiring accordingly.
Updates nf-test snapshots to reflect the new output structure.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
subworkflows/nf-core/differential_functional_enrichment/main.nf	Adjusts GSEA channel construction and adds aggregated artifact outputs for gprofiler2/GSEA.
subworkflows/nf-core/differential_functional_enrichment/meta.yml	Documents new outputs (`gprofiler2_artifacts`, `gsea_artifacts`).
subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test.snap	Snapshot updates for new outputs and metadata ordering.
subworkflows/nf-core/abundance_differential_filter/main.nf	Adds `plots` + `other` channels and minor closure style tweaks.
subworkflows/nf-core/abundance_differential_filter/meta.yml	Documents the new outputs (`plots`, `other`).
subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap	Snapshot updates for new outputs and metadata.

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subworkflows/nf-core/differential_functional_enrichment/meta.yml

subworkflows/nf-core/abundance_differential_filter/meta.yml

subworkflows/nf-core/abundance_differential_filter/main.nf

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

…ore/modules into update-for-workflow-outputs

pinin4fjords

I'm very unconvinced by the channel combinations, can we leave them separate please to allow flexible usage? All you should really need to do here is add any outputs that currently don't go to channels, to support the workflow output syntax in the pipeline.

pinin4fjords · 2026-03-24T10:19:16Z

subworkflows/nf-core/differential_functional_enrichment/main.nf

+            GSEA_GSEA.out.rpt
+                .mix(GSEA_GSEA.out.index_html)
+                .mix(GSEA_GSEA.out.heat_map_corr_plot)
+                .mix(GSEA_GSEA.out.report_tsvs_ref)


Did you intend to mix these here as well as above?

pinin4fjords · 2026-03-24T10:22:01Z

subworkflows/nf-core/differential_functional_enrichment/main.nf

-    decoupler_png = DECOUPLER_DECOUPLER.out.png
-
+    // main results
+    results = ch_results


I'm unconvinced by outputting everything in a single channel this way. You're mixing channel 'arity' and forcing anyone who wants to access specific channels to sort though a heterogenous set. Can we leave these separate please, and defer any combinations to the workflow?

yes.. i was trying to see if i can simplify, but didnt like it either. reverting back to the previous commit now.

pinin4fjords · 2026-03-24T10:37:09Z

e.g. here's how I prepared subworkflows for workflow output syntax: #9765

Essentially just making sure that everything was available via channels. No need to combine everything artificially into a small number of outputs.

suzannejin · 2026-03-24T11:10:55Z

hi @pinin4fjords , sorry for the confusion, i was trying to see if extra simplification works, but it did not.
Just reverted back to the previous commit, this should work for the workflow output migration purpose.

pinin4fjords · 2026-03-24T13:51:25Z

subworkflows/nf-core/abundance_differential_filter/main.nf

+    ch_plots = DESEQ2_DIFFERENTIAL.out.dispersion_plot_png
+        .mix(LIMMA_DIFFERENTIAL.out.md_plot)
+
+    ch_other = DESEQ2_DIFFERENTIAL.out.rdata


Sorry to be a pain, thinking about this we should probably emit disparate things separately, the 'other' doesn't really work. If I want the session info in a consuming workflow I don't want to have to filter it out.

I'm inclined to say the same about the plots unless they're equivalent plots (which I don't think is the case here).

I splitted the output for the ABUNDANCE_DIFFERENTIAL_FILTER subworkflow.
Now, for the GSEA artifacts, you want to emit a different output for each of the 21 artifacts?
That's a lot of duplicated verbosity to deal with at all subworkflow, workflow levels.

It just doesn't make sense to combine disparate things into channels. I agree the current implementation makes things awkward- it's why I put this PR on hold for rnaseq: nf-core/rnaseq#1679

Nextflow will have some improvements, notably record types, that may help this soon. It's fine to put this on pause until that happens if you feel the same here as I did for rnaseq.

The migration here is mainly needed to solve this issue affecting pipeline cache.
That's why I wouldn't pause it for this PR. I'd vote to have a less perfect subworkflow output structure for the moment (it can always be adapted later on).

Could you explain why separating the outputs would block that work?

What meant is that pausing the migration will block that work, not splitting the output itself.

However, the entire idea about pipeline hub is that alternative methods (in this case functional enrichment) can be exchanged easily. This means adding a new method will ideally only require changes in the subworkflow, not the pipeline itself. By splitting outputs, instead of classifying outputs into the same category, will make this even more difficult.

But yes, i agree that having them in artifacts/other is also not ideal. I will split the outputs as temporal solution. With syntax improvements in the future this may be better addressed.

When different methods have clear analogs, putting them in the same channel makes sense (perhaps after some normalisation of the structure- for future). But combining e.g. size factors and session info will never make sense at the component level.

pinin4fjords · 2026-03-26T10:35:15Z

subworkflows/nf-core/differential_functional_enrichment/main.nf

    gprofiler2_all_enrich = GPROFILER2_GOST.out.all_enrich
    gprofiler2_sub_enrich = GPROFILER2_GOST.out.sub_enrich
-    gprofiler2_plot_html  = GPROFILER2_GOST.out.plot_html
+    gprofiler2_artifacts = GPROFILER2_GOST.out.plot_png


Same deal with these things. Arguably makes sense to group e.g. plots and reports, but we shouldn't be combining all the disparate things

To be fair, I know why you want to do this- I wanted something similar when I opened nextflow-io/nextflow#6756, i.e. to have channels mapping directly to publish locations.

But we can't make assumptions in components about how pipelines will want to publish.

ok nice it looks like with records, things will become easier.

pinin4fjords

Better- thanks!

update modules

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Copilot AI review requested due to automatic review settings March 23, 2026 18:59

suzannejin requested a review from pinin4fjords as a code owner March 23, 2026 18:59

github-actions bot added the size/l label Mar 23, 2026

Copilot started reviewing on behalf of suzannejin March 23, 2026 19:00 View session

Merge branch 'master' into update-for-workflow-outputs

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Copilot AI reviewed Mar 23, 2026

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suzannejin and others added 3 commits March 23, 2026 20:10

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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

fix changes

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Merge branch 'update-for-workflow-outputs' of https://github.com/nf-c…

2957563

…ore/modules into update-for-workflow-outputs

github-actions bot added the size/m label Mar 23, 2026

suzannejin enabled auto-merge March 23, 2026 19:30

pinin4fjords requested changes Mar 24, 2026

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suzannejin force-pushed the update-for-workflow-outputs branch from 55f1d16 to 2957563 Compare March 24, 2026 10:59

pinin4fjords reviewed Mar 24, 2026

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split outputs in abundance_differential_filter and update snapshots

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suzannejin force-pushed the update-for-workflow-outputs branch from 03506ff to 729a7c3 Compare March 24, 2026 14:56

Merge branch 'master' into update-for-workflow-outputs

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pinin4fjords reviewed Mar 26, 2026

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suzannejin added 2 commits March 26, 2026 16:46

split outputs in subworkflow differential_functional_enrichment

685596f

Merge branch 'master' into update-for-workflow-outputs

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pinin4fjords approved these changes Mar 26, 2026

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suzannejin added this pull request to the merge queue Mar 26, 2026

Merged via the queue into master with commit 2f1b98c Mar 26, 2026
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suzannejin deleted the update-for-workflow-outputs branch March 26, 2026 16:49

suzannejin mentioned this pull request Mar 27, 2026

migrate to new workflow outputs nf-core/differentialabundance#662

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suzannejin commented Mar 23, 2026 •

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