What should the output of this repository be?

[gwaybio]

In my vision, the purpose of the repository is to store the code we used for data downloading and processing, but we don't actually require a user to run it all.

We could provide a link to a versioned figshare url storing the processed datasets. Or maybe we could even build a python package to quickly fetch the data in some sort of matrix form already. We can build upon these ideas here.

Either way, I do not think its necessary for intermediate or final output files to live here.

[jaclyn-taroni]

I'm assuming that your concern is file size -- likely too big for git lfs?

We could provide a link to a versioned figshare url storing the processed datasets. Or maybe we could even build a python package to quickly fetch the data in some sort of matrix form already.

I'm down with both of these options. I think ideally we would do both rather than one or the other.