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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
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Dev version: On parameters website list parameter gene_sets_files in section GSEA #243

Open aghr opened 4 months ago

aghr commented 4 months ago

Description of feature

I noticed that in the dev version the GSEA parameter --gsea_gene_sets disappeared and now one should use --gene_sets_files. I'd have two suggestions:

  1. For backward compatibility keep the parameter gsea_gene_sets next to gene_sets_files so users won't need to change there parameter files when working with different versions of the pipeline.

  2. Move the description of the parameter gene_sets_files from on the webpage from section 'Options related to gene set analysis' to section 'GSEA' so users find it more easyly when searching for info on GSEA configuration.

WackerO commented 3 months ago

Hey @aghr, so the issue is that this param is now used as the central parameter for accepting gene set files for both GSEA and gprofiler (and possibly other tools in the future). That's why it shouldn't be moved to GSEA. The backward compatibility is interesting, is this something that's done in nf-core pipelines? I'm however also a bit hesitant to do this as it will clutter the pipeline even more with parameters. I think when switching to a new pipeline version, users should have a look at the updated params and check if something changed...