1.1.0-rc

v1.1.0-rc1:

Support for read groups:
Support ‘pool’ read groups taken from BED file, e.g.:

• nCoV2019_1
• nCoV2019_2
  These can be helpfully viewed in the Tablet viewer.
  Do variant calling separately on each group, permits detection of incongruent mutations e.g. from contamination

Update to nanopolish 0.12.5 fo more informative VCF output
Change nanopore filtering to support new VCF output (e.g. strand-bias)

Support indels with bcftools consensus
Longshot added to Medaka to permit filter VCF on depth

New workflow model - all commands run "one per sample", script nanopolish index

Add 'artic gupplyplex' for support for demultiplexed Guppy output to replace 'artic gather'

Fix for align_trim to remove erroneous CIGAR strains that can cause medaka to fail

Support for amplicons v3 format file (Will Rowe)

Test suite (Will Rowe)

Documentation (Will Rowe)

Remove old deprecated code (Will Rowe)