Replace set_final_strain_name.py

[victorlin]

initially brought up by @joverlee521 in nextstrain/dengue#12 (comment) and resurfaced on Slack

The script is a not-so-ideal workaround for the problems that come from using a custom metadata ID column. Better solutions:

• export v2: Add option to choose sample name from metadata augur#1264
• Extend usefulness of tip labels auspice#1668

Update pathogen repos

GitHub search reveals this is used in:

• nextstrain/mpox · nextclade/scripts/set_final_strain_name.py, phylogenetic/scripts/set_final_strain_name.py
  • Use accession for node name but display strain mpox#275 (only for phylo, not nextclade)
• Default tip label zika#72
• nextstrain/rsv · scripts/set_final_strain_name.py
• nextstrain/lassa · phylogenetic/scripts/set_final_strain_name.py
• nextstrain/dengue · phylogenetic/scripts/set_final_strain_name.py
• nextstrain/oropouche · phylogenetic/scripts/set_final_strain_name.py

[victorlin]

nextstrain/auspice#1668 has been merged and released. I'm not sure what the next step is for this issue. From @joverlee521 nextstrain/augur#1264 (comment):

Then we would need to add tip_label as an allowed property for display_defaults in our auspice config schema.

I also think export v2 should verify the tip_label field is an available node_attr or automatically add it as a node_attr if the field is available in the metadata file.

Is nextstrain/augur#1264 still useful?

[joverlee521]

Is nextstrain/augur#1264 still useful?

Thanks for flagging @victorlin! Closed nextstrain/augur#1264.

Then we would need to add tip_label as an allowed property for display_defaults in our auspice config schema.

Looks like this was added in nextstrain/augur@6ce1bf7.

I also think export v2 should verify the tip_label field is an available node_attr or automatically add it as a node_attr if the field is available in the metadata file.

I still think this would be nice, but not prioritized.