Updating snakefiles for analysis of ihmp data

[brooksph]

@taylorreiter and @luizirber the snakefiles for downloading and calculating signatures for the ihmp IBD data are here on the ihmp branch. Per our discussion today these files may change significantly if we skip the download in favor of using the s3 bucket. The following should also be done:

• Create rule for assembly with MEGAHIT
• Add flag "extract-unclassified" to gather rule "calculate_signatures"
• Create rule for contig annotation with Prokka
• Remove rules referring to LCA gather
• Add rule for KEGG annotations?

[taylorreiter]

The KEGG annotation need to be done manually here, but I'll add rules to parse the output.