mm39 endpoint is hard coded

[rbpatt2019]

Currently, the mm39 end point is hardcoded into the pipeline. We (should) be able to grep the desired end version out of the provided gtf link then get the proper endpoint from Liftover automatically.

This will require restructuring the config, as well as expanding some rules in common.py to automatically handle this.

[rbpatt2019]

Some further inspections shows that this isn't entirely true. The names of the rules certainly make it seem this way, but, as all URLs are provided by the user, the pipeline will handle any conversion as long as all the endpoints are consistent. That is, if you want to lift onto XX, then you download an XX GTF, FASTA, and the mm10 to XX liftover file.

I'm going to leave this open for future development. I think we could handle this better. Most of the default sources have very well structured URLs. Maybe we could simply ask for the species and build, then construct the paths ourselves.