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Remove parameter --gsea_run #239

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aghr opened this issue Feb 20, 2024 · 1 comment
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Remove parameter --gsea_run #239

aghr opened this issue Feb 20, 2024 · 1 comment
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enhancement New feature or request

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@aghr
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aghr commented Feb 20, 2024

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.

@aghr aghr added the enhancement New feature or request label Feb 20, 2024
@WackerO
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WackerO commented Mar 18, 2024

Hey @aghr,
as mentioned in #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.

@WackerO WackerO closed this as completed Mar 18, 2024
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