Simplify pipeline parameters about differentialabundance HOT 3 OPEN

Hi @WackerO -- could this issue be caused by exploratory_assay_names? #196

I don't see --exploratory_assay_names listed here in the documentation:

But I do see it in the main branch:

from differentialabundance.

Something like exploratory_assay_names is not marked as a required param in the nextflow schema, but effectively it is, as if the param is not correctly set, the pipeline will fail.

That's just an oversight in the schema definition, please feel free to fix. But we should probably put this option and the suffix one (and similar) in a new 'Advanced options' section. This IS a parameter, even if the users don't change it, and it's nice for advanced user to tweak the suffixes if they want.

You'll notice that exploratory_assay_names is a hidden parameter to discourage users from changing it (which is why you can't see it in the UI @olgabot - you shouldn't need to interact with it). We could do the same with others.

The alternative is hard-coding all these things into the workflow code, which don't think would be an improvement.

Other params, like those for a GTF file (e.g. features_id_col), are expected even when the user does not input a GTF file.

That's because it's required in the absence of a GTF file - it's required everywhere we need to cross reference matrix rows with feature annotation (which is lots of places). If there is a context in which the pipeline can work without this parameter, feel free to highlight it, and we can make the parameter optional (and add checks everywhere it's needed but not supplied).

from differentialabundance.