Merge pull request #58 from carlacummins/master

Updated help text
Add IVA assembler
Merge pull request #59 from martinghunt/add_iva_assembler

Add IVA assembler
Remove debugging copying of conf file
Use different defaults for IVA assembly options
Merge pull request #60 from martinghunt/add_iva_assembler

Add iva assembler
Merge pull request #61 from carlacummins/master

Added option to omit assembly and annotation configs for bacteria_register_and_qc
Removed generation of qc config files from form all of the Mapping, RnaSeq, SnpCalling steps
fix command logging
Revert "Removed generation of qc config files from form all of the Mapping, RnaSeq, SnpCalling steps"

This reverts commit db975217c6d5f434eb18054c227dc100a1929daa.
fix tests for qc config and logging time
Merge pull request #62 from andrewjpage/fix_failing_tests

Fix failing tests
allow for multiple assemblies
Merge pull request #63 from andrewjpage/multiple_assemblies

allow for multiple assemblies
increase assembly limit to 1000
Merge pull request #64 from andrewjpage/increase_assembly_limit

increase assembly limit to 1000
Add kraken_db to QC conf files
Merge pull request #65 from martinghunt/add_kraken_to_qc

Add kraken_db to QC conf files
Edited version numbers
Merge remote-tracking branch 'sanger-pathogens/master'