2.1.0 - Performance, security and scientific correction

• Update base image to dockstore-cgpwxs:3.1.6 (from 3.0.3)
  • Includes, memory footprint reduction for Caveman flagging
  • Significant speedup in indel input generation
  • Parallel flagging for SNV
  • Fragment based SNV/Indel calling
• Upgrade allele counter and brass
• Reduce number of layers in final image.
• Remove some legacy env vars from wrappers
• Battenberg removed
  • Was only included to do base allele counts not complete analysis
  • Underlying data files are not supported for new builds or other species
  • Contact original authors for ongoing support
• Wrapper script didn't explicitly specify sex SNP loci file (ASCAT)
  • no impact for GRCh37 other species/build would have used wrong sex chromosome SNPs
• CaVEMan step wasn't being passed normal contamination value, scientific impact:
  • previously caveman.pl default of 0.1 was applied
  • this will now honor the value from ASCAT (1-$rho)