clades.tsv files

[dsobral]

I'm probably missing something, but I was expecting to find config/h1n1pdm/ha/clades.tsv or config/vic/ha/clades.tsv (like I find for h3n2).

Nonetheless, many of the profile yaml files refer to those files.

Thank you,
Daniel

[huddlej]

Hi @dsobral, these clades files used to live in this repository, but now they live in the corresponding repositories of the influenza clade nomenclature organization. This repo's workflow downloads the clades files from GitHub prior to running augur clades, so we can refer to these local paths in our YAML configuration files.

If you run the example build mentioned in this repo's README, you'll see a download_clades rule that runs curl to grab the clades TSV like this:

curl -o config/h3n2/ha/clades.tsv "https://raw.githubusercontent.com/influenza-clade-nomenclature/seasonal_A-H3N2_HA/main/.auto-generated/clades.tsv"

[dsobral]

Thanks! That's great.

I just got a bit confused because the file is there for H3N2 but not for the others.