use only one genome

[ChristopherBarrington]

• removes genomes as a list of stanza and uses only one _genome
• updates guess parameters script
• updates get (parse) parameters utility; fixes ordering and default values
• updates workflows, no longer need to check for genome version
• updates genome preparation
• remove unique id parameter, now dataset id is unique
• remove genome name key, use assembly or id
• remove index path from non-quantification workflows - fasta/gtf supplied in the genome