split outputs

[suzannejin]

PR checklist

Closes #XXX

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[Copilot]

Pull request overview

This PR updates the DIFFERENTIAL_FUNCTIONAL_ENRICHMENT subworkflow to split/reshape enrichment outputs into more granular emitted channels (rather than large “artifacts” mixes), while also exposing some generic outputs.

Changes:

• Refactors emitted outputs for g:Profiler2 and GSEA into multiple, more specific channels.
• Adds “generic” emitted channels for rds and session_info.
• Refactors version collection wiring to align with the new output structure.

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[Copilot]

gsea_gene_set_info joins multiple optional outputs with remainder: true and is emitted as-is. This will produce tuples containing null entries for missing optional files (tsv/html/png/enplot/dist), which is error-prone for consumers and awkward to document. Consider mapping to a list of present files (dropping nulls) or splitting these into separate emitted outputs.

Suggested change

	.join(GSEA_GSEA.out.gene_set_dist, remainder: true)
	.join(GSEA_GSEA.out.gene_set_dist, remainder: true)
	.map { row ->
	/*
	* row is a tuple of the form:
	* [meta, gene_set_sizes, gene_set_tsv?, gene_set_html?,
	* gene_set_heatmap?, gene_set_enplot?, gene_set_dist?]
	* where optional entries may be null due to `remainder: true`.
	* Keep meta as-is and collect only non-null file outputs.
	*/
	def (meta, *files) = row
	def present_files = files.findAll { it != null }
	tuple(meta, present_files)
	}

[Copilot]

The emit: outputs were renamed/restructured here (e.g., gprofiler2_plot_html -> gprofiler2_html, gsea_report/gsea_artifacts -> gsea_report_tsv/gsea_html/gsea_plots/etc., and new generic rds/session_info). However, subworkflows/nf-core/differential_functional_enrichment/meta.yml and the nf-test snapshots still describe/assert the old output names and shapes, so linting/tests will fail until they are updated to match the new emit: interface.

[Copilot]

These join(..., remainder: true) results are emitted directly. When the optional RHS outputs are absent (e.g. sub_enrich / sub_plot), Nextflow join will emit tuples containing null placeholders, which can break downstream consumers that assume only file paths. Consider mapping the joined tuples to remove nulls (e.g., emitting a list of existing files) or keep optional outputs as separate emitted channels.

[Copilot]

gsea_html / gsea_plots are built by chaining join() calls and then emitted. Because snapshot and butterfly_plot are optional, the remainder: true joins will introduce null placeholders in the emitted tuples when those files are not produced, which can cause downstream .map { meta, file -> ... } / file() usage to fail. Consider normalizing these outputs (e.g. emit [meta, List<Path>] with nulls removed, or emit optional files on their own channels).

Suggested change

	.join(GSEA_GSEA.out.snapshot, remainder: true)
	gsea_plots = GSEA_GSEA.out.histogram
	.join(GSEA_GSEA.out.heatmap)
	.join(GSEA_GSEA.out.pvalues_vs_nes_plot)
	.join(GSEA_GSEA.out.ranked_list_corr)
	.join(GSEA_GSEA.out.butterfly_plot, remainder: true)
	.join(GSEA_GSEA.out.snapshot, remainder: true)
	.map { meta, report_ref, report_target, index_html, heatmap_corr, snapshot_opt ->
	def files = [report_ref, report_target, index_html, heatmap_corr, snapshot_opt].findAll { it != null }
	[meta, files]
	}
	gsea_plots = GSEA_GSEA.out.histogram
	.join(GSEA_GSEA.out.heatmap)
	.join(GSEA_GSEA.out.pvalues_vs_nes_plot)
	.join(GSEA_GSEA.out.ranked_list_corr)
	.join(GSEA_GSEA.out.butterfly_plot, remainder: true)
	.map { meta, histogram, heatmap, pvalues_vs_nes_plot, ranked_list_corr, butterfly_opt ->
	def files = [histogram, heatmap, pvalues_vs_nes_plot, ranked_list_corr, butterfly_opt].findAll { it != null }
	[meta, files]
	}