v1.6.3

Added support for Nextclade v3+ and associated datasets:

• Updated lineage assignment rules within SIGNAL all for Nextclade v3+ support
• Backwards compatibility maintained between v3 and v2 in both software and datasets where both can be specified via the yaml configuration file
• Includes fix where Nextclade version, when specified, would not update as requested
• Nextclade dataset tag will now be properly identified when reporting final versions of software and datasets, if not specified by the user
• Updated general format of the yaml configuration file for clarity on Nextclade parameters (reflected when using signalexe.py --config-only). Parameters remain unchanged. See below:

# Versions for Nextclade (software & datasets)
# nextclade: Software version. Input should use numbers only (i.e., 2.14.0)
# nextclade-data: The nextclade dataset tag. Refer to available nextclade datasets. Accepted tag format is 'YYYY-mm-ddTHH:MM:SSZ'
# Be as specific as possible with the desired dataset tag. Can accept dates (YYYY-mm-dd) alone, but will assume corresponding timestamp (HH:MM:SS). SIGNAL will automatically adjust between v2 and v3 dataset tag formats
# Leave blank for latest versions
nextclade:
nextclade-data:

# Nextclade v2 only
# nextclade-include-recomb: set to False will download the recombinant-sequence free version of the nextclade dataset
nextclade-include-recomb: True

General updates:

• General performance update allowing mamba to be used when updating lineage assignment software
• Updated dependencies for SIGNAL postprocess