nextstrain / dengue

Nextstrain build for dengue virus
https://nextstrain.org/dengue
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ENH: Generalize taxon id to serotype map definitions to a configuration file #27

Open j23414 opened 5 months ago

j23414 commented 5 months ago

Context

As a potential enhancement, it may be beneficial to allow users to configure the serotype (and taxon ID) list. This suggestion is inspired by the discussions in the following comments:

This would be particularly useful if we intend to permit users to modify the list of serotypes for curation, especially if taxon IDs become more detailed (e.g., the taxonomy subtree for Dengue).

Possible solution

Open to more suggestions or feedback here, but some solutions include:

  1. Store the list and map in a dedicated config/taxid_to_serotype_map.tsv file.
  2. Store the list and map directly in the config/build.config, following a similar approach to the NCBI field_map configuration.