Include original GISAID strain name in metadata #192
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Adds the GISAID strain name to list of fields to fetch from fauna in and parse from the raw sequences FASTA in the "upload" workflow. This change will include these original names in the metadata in S3.
Adds `gisaid_strain` to Auspice config JSONs for public and private Nextstrain builds, allowing users to display those original strain names as tip labels or search for samples by those names.
Sets the default tip label in public Nextstrain builds to the GISAID strain name. This change should reduce confusion for users who want to cross-check Nextstrain analyses with the original data in GISAID. This commit does not change the default label in private builds to minimize confusion when comparing genetic data to serological data by strain name.
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Below is an example view before and after setting the default tip label to the GISAID strain. Before: After: |
Minimize confusion for ourselves by removing lists of FASTA fields from builds that download parsed metadata and sequences from S3 and don't need these fields. We could easily get confused into thinking that new fields like `gisaid_strain` need to be added to each of these build configs when that isn't the case.
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I'm going to merge this to include GISAID strain names in the weekly ingest, but if we decide that the default tip label change here is a bad idea, it is easy to revert for future builds. |
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