initial commit
Merge branch 'master' of github.com:andrewjpage/Bio-VertRes-Config
Add assembly, import and store
Qc pipeline config files
Add mapping base
smalt mapping
BWA mapping
add all other available mappers, unsure if they work
use limits without escaping out
snp calling
RNA seq expression, TraDIS and BAM improvement
Add pipeline actions for top-level files
untested toplevel files and output configs
tests for creating top level files and configs
register a study
make config base required and pass in at higher level
Create global files
register and qc a study
bacteria snp calling pipeline
Add Bwa for bacteria snp calling plus a load of other untested mappers