Make nextclade tree

[kimandrews]

Description of proposed changes

This workflow creates a tree that can be used as part of a Nextclade dataset to assign genotypes to measles samples based on criteria outlined by the WHO

The tree created by this workflow includes N450 sequences for 28 reference strains defined by the WHO, along with other representative strains for each genotype that are obtained from the ingest output, using genotype assignments reported on NCBI. Genotypes are then assigned to each node with augur clades, using clade-defining mutations in defaults/clades.tsv.

Details regarding the workflow are described in a README.md

Related issue(s)

Checklist

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[trvrb]

This is wonderful @kimandrews! Cleanly constructed in terms of the workflow and the result looks great in terms of consistency of MeV Genotypes and amount of data used. I think this will work well as a Nextclade reference tree. I just made a few changes to the Auspice config for the Nextclade tree in the above commit.

[trvrb]

Will you be updating the workflow to create the full Nextclade dataset in the future? E.g. mpox's nextclade workflow packages the whole dataset.

Packaging up into a Nextclade dataset will be super useful. Would be nice to have this on the clades.nextstrain.org list.

Since there are a lot of shared files between phylogenetic and nextclade workflows, we could consider using a shared directory to hold these files, so we don't need to duplicate the files across two directories.

I personally don't mind the code duplication in this particular case. Easier for me to think about these as separate things. But it's not a strong preference.

[trvrb]

Looks like this may be ready to merge? @jameshadfield: Could you confirm?

[kimandrews]

Looks like this may be ready to merge? @jameshadfield: Could you confirm?

I talked with @jameshadfield yesterday and we are good to merge.