v2.1.0.0

• assemble_refbased changes [#83, #84]:
  • bugfix: workflows should never fail when no genome is produced. Empty output files are now properly emitted with no errors.
  • increase default min_coverage for consensus calling from 2 major allele reads to 3
  • bump ivar docker images to 1.2.2
  • update documentation
• build_augur_tree changes [#85, #90]
  • add augur clades task and integrate with main workflow
  • integrate existing augur filter task with main workflow
  • increase AUGUR_RECURSION_LIMIT to handle very deep/large trees
  • update documentation
• filter_bam_to_taxa bugfix for taxonomic_ids optional input [#92]
• add align_and_count_multiple_report for improved/bugfixed spike in count handling [#91]
• VM runtime reshaping [#88, #89, #92]
  • disable GCP preemption for certain long running tasks
  • expose disk size requirements for certain tasks and increase their default values
  • increase default RAM for rmdup_ubam task
• update viral-core (and downstream docker images) to v2.1.0