Add streptococcus workflow

[ryanjameskennedy]

Description

Summary of the changes made:

• Add emmtyper module
• Add streptococcus profiles
• Add emmtyper to Makefile
• Added emmtyper module process (emmtyper)
• Added emmtyper to Makefile
• Added downloading of Streptococcus & Streptococcus pyogenes files to makefile
• Added get_taxon to methods
• Added streptococcus and streptococcus_pyogenes workflows and profiles to configs
• Added ska filepath to yaml
• All modules can be called in one workflow -> profile determines whether they are actually executed using when statement
• Empty channels fixed
• Chewbbaca collection of input fixed
• Fixed resfinder --species arg
• Moved taxon related methods to methods directory
• Changed spyogenes genome from GCF_900475035.1 to GCF_000006785.2
• Changed containerDir filepath for Lund configs
• Updated PRP to version 0.11.0
• Update configs/nextflow.dev.config root fpath
• Changed the freebayes output directory

Primary function of PR

• [x] Major functionality improvement / New type of analysis

Testing

Tested on Streptococcus samples and saureus