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nf-core / differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
https://nf-co.re/differentialabundance
MIT License
57 stars 32 forks source link

Remove parameter --gsea_run #239

Closed aghr closed 6 months ago

aghr commented 7 months ago

Description of feature

For running a GSEA I would invoke min these two parameters --gsea_gene_sets XXXX --gsea_run true. To reduce the number of parameters it could make sense to remove --gsea_run true and run the GSEA if the user provides gene sets via --gsea_gene_set XXXX.

WackerO commented 6 months ago

Hey @aghr, as mentioned in https://github.com/nf-core/differentialabundance/issues/243, there is now also gprofiler which shares the gene set param but can be run independently, so it is necessary to have the gsea_run param to enable running either of the two enrichment tools (or none) even when providing a file. I'm closing this issue, feel free to reopen if you have any more input regarding this.