Add missing Taxonium link-outs - #1112
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corneliusroemer
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Aug 17, 2026
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Check a CCHF linkout, looks good. Taking down preview as we're starved and need raw reads/zika previews
theosanderson
marked this pull request as ready for review
August 21, 2026 16:26
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Claude finished @theosanderson's task in 3m 11s —— View job Code review
Config-only change, so the review is about consistency and correctness of the identifiers rather than logic. One thing worth fixing, three worth a look — all left as inline comments. Verified correct:
Not verified: network egress is blocked in this environment, so I could not re-check the 32 asset URLs myself or confirm whether |
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| - name: "Place on viral UShER tree (DENV-1)" | ||
| maxNumberOfRecommendedEntries: 2500 | ||
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/treetime_rerooted_NC_001477.1.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/treetime_rerooted_NC_001477.1.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-1|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 1}}" | ||
| - name: "Place on viral UShER tree (DENV-2)" | ||
| maxNumberOfRecommendedEntries: 2500 | ||
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_2/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_2/treetime_rerooted_NC_001474.2.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_2/treetime_rerooted_NC_001474.2.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_2/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-2|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 2}}" | ||
| - name: "Place on viral UShER tree (DENV-3)" | ||
| maxNumberOfRecommendedEntries: 2500 | ||
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_3/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_3/treetime_rerooted_NC_001475.2.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_3/treetime_rerooted_NC_001475.2.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_3/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-3|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 3}}" | ||
| - name: "Place on viral UShER tree (DENV-4)" | ||
| maxNumberOfRecommendedEntries: 2500 | ||
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_4/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_4/treetime_rerooted_NC_002640.1.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_4/treetime_rerooted_NC_002640.1.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_4/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-4|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 4}}" |
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The four dengue entries are missing category: "Viral UShER", while the Andes and CCHF entries added in this same PR do set it (lines 2507, 2644, 2648, 2652). Every other dengue link-out already carries a category (Nextclade, Sealion, Other), so these four will be the only uncategorised items in the dengue list and will render outside the grouping rather than in a "Viral UShER" group alongside the other organisms.
Suggested change
| - name: "Place on viral UShER tree (DENV-1)" | |
| maxNumberOfRecommendedEntries: 2500 | |
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/treetime_rerooted_NC_001477.1.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/treetime_rerooted_NC_001477.1.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-1|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 1}}" | |
| - name: "Place on viral UShER tree (DENV-2)" | |
| maxNumberOfRecommendedEntries: 2500 | |
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_2/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_2/treetime_rerooted_NC_001474.2.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_2/treetime_rerooted_NC_001474.2.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_2/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-2|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 2}}" | |
| - name: "Place on viral UShER tree (DENV-3)" | |
| maxNumberOfRecommendedEntries: 2500 | |
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_3/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_3/treetime_rerooted_NC_001475.2.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_3/treetime_rerooted_NC_001475.2.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_3/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-3|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 3}}" | |
| - name: "Place on viral UShER tree (DENV-4)" | |
| maxNumberOfRecommendedEntries: 2500 | |
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_4/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_4/treetime_rerooted_NC_002640.1.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_4/treetime_rerooted_NC_002640.1.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_4/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-4|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 4}}" | |
| - name: "Place on viral UShER tree (DENV-1)" | |
| category: "Viral UShER" | |
| maxNumberOfRecommendedEntries: 2500 | |
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/treetime_rerooted_NC_001477.1.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/treetime_rerooted_NC_001477.1.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-1|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 1}}" | |
| - name: "Place on viral UShER tree (DENV-2)" | |
| category: "Viral UShER" | |
| maxNumberOfRecommendedEntries: 2500 | |
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_2/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_2/treetime_rerooted_NC_001474.2.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_2/treetime_rerooted_NC_001474.2.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_2/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-2|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 2}}" | |
| - name: "Place on viral UShER tree (DENV-3)" | |
| category: "Viral UShER" | |
| maxNumberOfRecommendedEntries: 2500 | |
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_3/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_3/treetime_rerooted_NC_001475.2.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_3/treetime_rerooted_NC_001475.2.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_3/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-3|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 3}}" | |
| - name: "Place on viral UShER tree (DENV-4)" | |
| category: "Viral UShER" | |
| maxNumberOfRecommendedEntries: 2500 | |
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_4/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_4/treetime_rerooted_NC_002640.1.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_4/treetime_rerooted_NC_002640.1.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_4/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-4|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 4}}" |
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I think it would be good to add the categories
| url: "https://mapoplexus.genomium.org/?url={{[metadata]}}" | ||
| - name: "Place on viral UShER tree (DENV-1)" | ||
| maxNumberOfRecommendedEntries: 2500 | ||
| url: "https://www.taxonium.org/build?mode=no_genbank&startingTreeUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/optimized.pb.gz}}&refGbffUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/treetime_rerooted_NC_001477.1.gbff}}&refFastaUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/treetime_rerooted_NC_001477.1.fa}}&originalMetadataUrl={{https://angiehinrichs.github.io/viral_usher_trees/trees/dengue_virus_type_1/metadata.tsv.gz}}&fastaUrl={{[unalignedNucleotideSequences:DENV-1|fasta]}}&metadataUrl={{[metadata]}}&organism={{dengue virus type 1}}" |
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Nit: organism={{dengue virus type 1}} is lower-cased, whereas every other UShER link-out passes a capitalised name (Zaire ebolavirus, West Nile virus, Yellow fever virus, Monkeypox virus clade Ia). This string is shown in the Taxonium UI, so it will read as inconsistent — Dengue virus type 1 would match. Applies to all four dengue entries.
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Summary
Why
Matching trees and reference assets are now published in the viral UShER tree catalogue, but these Pathoplexus organisms did not expose them through Link Outs. This lets users send selected sequences directly to Taxonium for placement and visualization.
Bundibugyo Ebola remains excluded because there is no matching published viral UShER tree.
Validation
loculus_values/values.yamlsuccessfully with YAML aliases enabledgit diff --check🚀 Preview: Add
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