Minimum hardware specs are hard to give without further information about what is acceptable running time. Most analyses would run on old or cheap harware, but would simply take terribly long. The most important spec is memory size. Your genome, as indexed by the read mapper should fit in memory, that's what can be said without further details of genome size and software. Hardware Suitable For Generic Nextgen Sequencing Processing? seems to still be valid, just double the RAM figures. Otherwise, get as many CPU cores and fastest IO as you can afford. You will need a lot of disk space as well.
Other things to consider:
- Support, system admin
- disk space
- do you really need a single new server for this, e.g. Is cloud an option, can you use existing large servers for this?
To echo what Michael posted: You'll need to be quite clear on the size of your genomes (you'll need something with a lot of RAM and storage memory for plant genomes) and what you want to do at your workstation (will you be doing transcriptome assembly or just SNP calling?). Once you have an exact idea of what you'll be doing and the time frame you need for your analysis, then you can plan for the specs of your workstation. Storage For Miseq In-House may be some help in addition to the one that Michael posted.