Unnecessary computation in de novo workflow

[donovan-h-parks]

When one specifies the --ar122_ms (renamed to --archaea in latest PR) flag, the MSA for identified bacterial genomes is still calculated. This is odd behaviour since I think specifying the --ar122_ms flag should imply that only archaeal genomes be processed through the workflow. In fact, I've changed these flags to --bacteria and --archaea to make it clear that the intent here is to restrict processing to a single domain.