v0.9.9-gamma

Release based on the BCG branch. Changes include:

1. changes to the logic in identify_tophits_and_contaminants.py. Centered around identifying M. bovis based on the name "Mycobacterium tuberculosis variant bovis" leading to using tuberculosis as the reference.
2. As above, but adding logic to identify bovis based on its lineage (LA.1).
3. Changes to the pipeline so that every sample has allelic depth calculated
4. VCFMIX now runs on minos VCF, added in tweak to accept that style of VCF file
5. changes to containers to align with the above
6. Changes to workflow logic to correct bugs when running with a mixture of MTB and NTM samples
7. Update to parse_kraken_report.py to deal with some kraken hits having non-alphanumeric characters

What's Changed

• another change to containers by @WhalleyT in #94
• update config by @WhalleyT in #95
• Recursive decontamination by @WhalleyT in #96
• update tests by @WhalleyT in #98
• update final report to accept QC sucesses by @WhalleyT in #99
• Tbtamr by @WhalleyT in #100
• Collate by @WhalleyT in #101
• config by @WhalleyT in #102
• Empty vcfs by @WhalleyT in #106
• Ntmprofiler by @WhalleyT in #107

Full Changelog: v0.9.9-beta...v0.9.9-gamma