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Release 1.0.0
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@AmandaBirmingham AmandaBirmingham released this 12 Mar 23:41
· 473 commits to main since this release
1.0.0
77738ed

New features:

  • provide additional output metadata (e.g., sequence run name, ivar software version) for each processed sample
  • report a new “indel flag” for any consensus sequence with insertion or deletion counts that are not evenly divisible by 3
  • fail acceptance for any sequence with a true indel flag
    *store a cumulative set of indel-failing consensus sequences and their qc results for later manual review by non-CCBB personnel
  • parameterize whether to include sequences from all sequencing runs or only from helix sequencing runs in lineage calling and optional subsequent tree building
  • unless processing for helix, include static set of historical consensus sequences in lineage calling and optional tree-building
  • automatically update pangolin before each lineage calling run
  • produce a csv containing qc/acceptance info for both accepted and rejected (cumulative) consensus sequences (see helix limitation above) as well as lineage calls for only accepted sequences
  • provide ability to run lineage calling without tree-building
  • modify pipeline parameters to better scale for very large sequencing runs
  • expand unit test suite
  • add continuous integration to github repository to run python unit tests on each check-in
  • move pipeline and data onto new return-to-learn governed AWS account
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