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@trvrb trvrb released this 17 Jun 19:59
· 201 commits to master since this release
v13
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From the change log:

  • 16 May 2023: Update workflow to support Augur v22 which updates the augur clades interface and structure of the output files to allow specifying the clade label & coloring keys. Because we use custom scripts to parse these files this worflow also needed updating. This change results in a simplifying of the nCoV pipeline (PR 1000).

  • 11 April 2023: Elevate XBB.1.16 as new clade 23B. See PR 1059 for the rationale behind this clade update.

  • 6 April 2023: Update conda environment dependencies: augur 19.2.0 -> 21.1.0, nextalign/nextclade 2.9.1 -> 2.13.1, iqtree 2.2.0_beta -> 2.2.0.3. PR 1056

  • 16 March 2023: Add a build configuration option, nextclade_dataset, to allow users to change the Nextclade dataset used for alignment and quality control. For example, setting nextclade_dataset: sars-cov-2-21L will use the BA.2 (Nextstrain 21L) dataset that provides immune escape and ACE2 binding scores. See the workflow configuration guide for more details. PR 1046

  • 30 January 2023: Include new clade 23A correspoding to Pango lineage XBB.1.5. See PR 1043 for the rationale behind this clade update.

  • 9 December 2022: Add immune escape and ace2_binding from metadata as colorings for nextstrain-open and nextstrain-gisaid builds. PR 1036

  • 24 November 2022: Add "1m" timespan in Nextstrain profile builds. PR 1027

  • 24 November 2022: calculate_delta_frequency: Allow script to work with fewer pivots available than requested with --delta-pivots. PR 1027

  • 4 November 2022: Deploy individual builds to Nextstrain as soon as they are ready, as opposed to only once all builds are ready to speed up the feedback loop PR #1025

  • 3 November 2022: Use weekly grouping for "2m" timespan in Nextstrain profile builds. PR 1023

  • 2 November 2022: Make RBD levels filterable PR 1028

  • 21 October 2022: Implement RBD-level coloring for BA.2 (21L) descendants. For background on this and lineage definitions please see Variant report 2022-10-17. PR 1018.

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