Automatic build of gene set database

[suzannejin]

Why and goal

Currently, if one wants to run functional analysis, the pipeline expects the user to give a gene set file as input.
It would be nice to have some modules that automatically create this file based on the genes in the input expression data.
Thi step could be added as part of the functional analysis subworkflow #384

Some ideas

• gProfiler2 can create a database when not provided. Maybe this can become a explicit step before running any functional analysis method.
• Use omnipathdb, as suggested by @grst
• Extend nf-core/modules mygene, to go beyond creating GO term based database.

[grst]

Have you also considered omnipathdb? It contains a wide range of databases including PROGENy, collecTRI, GO, CytoSig (see also #367) and can be queried using R, Python or a web API.

[suzannejin]

Have you also considered omnipathdb? It contains a wide range of databases including PROGENy, collecTRI, GO, CytoSig (see also #367) and can be queried using R, Python or a web API.

I have not considered it before, but it definitely looks like a possibility! Thank you for the suggestion!