1.1.0 - Result reproducibility, I/O and runtime improvements

BRASS updates

• Significantly reduces the run time of brass_group phase
  • see v6.0.0
  • Requires new version of the CNV_SV reference archive
• Ensure stable result between replicate runs:
  • see v6.0.2

Other dependency updates

• Based on dockstore-cgpwxs:2.1.1
  • Update caveman, pindel and vagrent to improve reproducibility.
  • Reduced I/O in caveman.
• Updates to alleleCount:v3.3.0 to improve access pattens for dense loci counting, resulting upgrades to:
  • ascatNgs:v4.1.0
  • cgpBattenberg:v3.1.0

Workflow updates:

• Reorganisation of some processes to reduce run-time:
  • Changes to alleleCount have vastly improved I/O pattern and reduced runtime for
    ascat and IMPUTE-allele counts (pre-Battenberg).
  • Reduced number of split files for IMPUTE-allele counts as reduced run time negates need for large spread
  • Reduced alleleCount runtim allowed reorganisation of processes reducing runtime on example data from 23h to 19.5h (28cpu).
• Added cavereads to example json specifying a higher value than default to reduce jobs required.