Allow addition of unreleased INRB data

[jameshadfield]

These changes are to allow addition of private metadata + sequences to be spiked into the build (after filtering but prior to subsampling). They are intended for use by INRB using an excel + fasta file which they maintain. As such, these changes probably shouldn't be merged into our canonical mpox repo, but perhaps we fork the repo into the INRB organisation and maintain these (small) changes there?

If you have access to the test xlsx + fasta (see this internal slack thread) then you can run from within the phylogenetic directory via:

1. python scripts/curate_private_data.py --sequences <fasta file> --xlsx <xlsx file> --remap-columns 'accession:accession' 'accession:strain' 'collection date:date' 'province:division' 'health zone:location' --fasta-header-idx 1
2. nextstrain build . --configfile defaults/clade-i/config.yaml --config private_data=true auspice_config=defaults/clade-i/auspice_config_inrb.json -f results/clade-i/good_metadata_combined.tsv auspice/mpox_clade-I.json

to do

• Metadata values need updating (e.g. they have "Homo-sapiens" we have "Homo sapiens")
• Fork into INRB repo?
• Test from INRB

[huddlej]

This review is just of the test commands and ability of the workflow to produce a tree and not a full code review or phylogenetic review.

The test commands worked for me from an ambient Nextstrain Conda environment after I ran the following commands:

# Needed to install dependencies not in Nextstrain env.
conda install openpyxl

# Needed to make data dir in fresh clone of mpox repo.
mkdir -p data/

After those commands, both the test commands ran without issue and the output tree from the workflow had the private data included as expected. 🎉

I was surprised to see that the output sequences and metadata from curate_private_data.py had default values instead of required values, but I see that the workflow expects those specific default names. Do you want to allow users to configure those names in the workflow config file? If they change the defaults, the workflow won't work as expected, so you could drop those output options completely and force the defaults.

Other minor comments included below.