Add some comments
Fix median coverage parameter for sga mode
Merge branch 'testing'

Adds functionality to remove temporary files
Scripts using blastn of windows around a variant to compare calls on different reference sequences
Change default params to work on 300bp contigs (default minimum from other scripts)
parse_qc_metadata.pl: allow use of regex to extract only certain strains
Create assembly module, move filter contigs sub to it
Add in improvement, annotation functions
Add wrappers to run assembly and annotation on large batches of bacterial read data (untested)
Corrected wrapper locations
Fix incorrect die on mkdir command return
Fix location of assembly pipeline in require
Fix unremoved line break breaking symlinks
batch assemble: improvement stage works in /tmp
Fix filtered contig name. Redo placement of tmp files from improvement pipeline
Change directory of annotation
Change default memory. Fix location of annotation logs
Improvements to job id log output
Reduce default number of threads, and add requirement to /tmp space
Allow user to set tmp dir for spades. Fix spades threads used