SnakeMake support for Mouse

[davmlaw]

Previously, the Bash scripts supported mouse. I am not sure of the state of the remaining bash scripts:

https://github.com/SACGF/cdot/tree/main/generate_transcript_data/Mus_musculus

It is probably possible to use a different YAML file for mouse, then pass that to the snake file and have it support mouse but I haven't tried it yet

If not, fix it.
If so, then add the basic mouse versions to the release data uploads

[YasirKusay]

Some issues that I discovered when running `generate_transcript_data/Mus_musculus/refseq_transcripts_grcm39.sh:

1. File above needs to be run from the root of this repo and not directly in the location of that script.

2. I changed the filename and url variables to download a gff file from ensembl. However, the ${BASE_DIR}/cdot_json.py gff3_to_json failed. However, changing this command to ${BASE_DIR}/cdot_json.py gtf_to_json would work if we supplied a gtf file from ensembl.

3. Will help if you mention where we can get the ${SPECIES}.gene_info file: https://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/Mus_musculus.gene_info.gz