Restructure

[KateSakharova]

New schema was developed (attached pipeline-overview.png)

• added rRNA detection step
• added get_core_genes step
• moved Eggnog and IPS
• removed step translate_genes
• added some tests and test-files
• mmseq subwf now has 2 different runs: for cutoff 0.9 (it's results go to functional annotation) and the rest params (0.95, 1.0, 0.5)
• added prokka subwf that cuts contig name because of prokka https://github.com/tseemann/prokka/issues/135

  Contig ID must <= 37 chars long: MGYG000000001_1-length-270477-cov-26.866771
  [18:01:26] Please rename your contigs OR try '--centre X --compliant' to generate clean contig names.

[mberacochea]

We need to add the license to all the code files, I've included the snippet in a comment. Not a priority but should be done when stable.