v12

From the change log:

• 1 July 2022: Update workflow to support Nextclade v2 (PRs 963, 969). See the Nextclade changelog for more information.

• 1 June 2022: Add "2m" timespan in Nextstrain profile builds. PR 957

• 29 April 2022: Include multiple timespans in Nextstrain profile builds. PR 910

• 29 April 2022: Update default mask parameters to mask 200 bases from the end of the genome rather than the existing 50. This was necessary because there is a large deletion in this region in circulating 21L viruses. This deletion is causing problems with alignment and the resulting mis-alignment appears as excess mutations in the tree. PR 939.

• 27 April 2022: Include new clades 22A, 22B and 22C, where 22A corresponds to Pango lineage BA.4, 22B corresponds to Pango lineage BA.5 and 22C corresponds to Pango lineage BA.2.12.1. Please see PR 933 for rationale behind these clade updates.

• 27 April 2022: Convert to hierarchical clade definitions. This streamlines clade definitions significantly and makes it easier to understand clade relationships. Changes can be seen in defaults/clades.tsv and in PR 855. This feature requires Augur v14.0 or above. To upgrade Augur follow the installation guide at docs.nextstrain.org.

• 12 April 2022: Add support for numbers in build names. PR 524

• 11 April 2022: Update clade definitions to be robust to presence of lineage BA.4 and BA.5 viruses. PR #913

• 17 March 2022: Add Nextclade_pango column to metadata PR 892

• 8 Mar 2022: Support disabling clock filters in the refine step by setting clock_filter_iqd: 0 in the refine section. PR #884, Issue #852.

• 11 February 2022: Add colors to default Auspice config for Nextclade quality control columns and a filter for overall Nextclade QC status. PR #861.