Adding hg19 to 'assembly_name' parameter options and post processing

[angarb]

Problem

I need to run one set of samples with the hg19 reference genome for a collaborator. The pipeline is not currently fully equipped to run 'hg19'. (We do have the gtf and star indices already downloaded.)

Solution

• [ ] Add GRCh37 (hg19) as an option in the 'assembly_name' options.
• [ ] Add GRCh37 (hg19) to rmats docker image.
• [ ] Add necessary line(s) of code to @lmurba's post processing script.

Are there any other places that the 'assembly_name' parameter is used in the pipeline?

Implementation

[Vlad-Dembrovskyi]

If we ever need to add a new reference genome - there is a problem that in many places it is now hardcoded for GRCh38 or mm10.

For now we need to document all such cases to know what to change when the time comes.