Pipelining/Command Line Tool

[LeSasse]

At the moment, nimgen consists mainly of two modules: "expressions" (for loading and processing gene expression data and performing statistical analyses with some parcellated marker) and "smash" (for creation of surrogate nii parcellation files used to perform n correlation analyses with a "smashed" brain and obtain empirical p-values). However, both of these modules take care of quite a bit of "pipelining" i.e. saving outputs etc, whereas other pipelining tasks are left to the user.

I think I would like to cleanly separate the purely analysis based modules from the pipelining. The idea is to have an additional "pipeline" module where individual jobs are defined based on the scheduling system (i.e. HTCondor/juseless, slurm/jureca, multiprocessing/pc etc.) in individual submodules.

Ideally I would then like to be able to configure pipelines in a yaml file (i.e. inputs, outputs, analysis options, etc.) and run it using nimgen as a command line tool, i.e.:

nimgen run config.yaml

or something along those lines. Nimgen can create submit files and submit them then, and perhaps prompt me if I am sure I want to submit this with x amount of jobs.