Standardize `Snakefile` to match `viral.snakefile` and to accomodate new files

[taylorreiter]

• [ ] change Snakefile files and paths from underscores to dashes: In virus.snakefile I switched all the paths that I was in control over to dashes instead of underscores. The snakemake rule names and python variables still have underscores bc it messes with the syntax highlight and variable assignment to use dashes, but I think I should standardize this to all of the variable names in the workflows in this repo.
• [ ] update rule names and output file folders with _genbank
• [ ] update sourmash sketch output with scaled and alphabet information
• [ ] drop s from samples wildcard
• [ ] add benchmarking for compute recommendations

[taylorreiter]

I could think about sketching everything at scaled 100 and then downsampling to scaled 1000 for subsequent operations in the original snakefile?