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@nextstrain-bot nextstrain-bot released this 10 Mar 19:45
3.20.0
9518cdd

3.20.0

Nextclade Web: show genome coverage outline behind "too many markers" message

When viewing dense regions with many mutations, the sequence view shows a "too many markers" message. The genome coverage outline is now visible behind this message, providing context about sequence coverage even when individual markers cannot be displayed. See #1759, #1760 for details.

Nextclade schemas: typed dataset attributes field

Dataset attributes (attributes field in pathogen.json and dataset index) have been refactored from free-form key-value pairs to typed structs with explicit fields. The new structure provides better validation and documentation for dataset metadata fields like name, reference name, reference accession, and clade. The previous free-form attributes map is no longer supported.

Nextclade schemas: cleanup

Several deprecated and unused fields have been removed from the dataset schema:

  • Removed enabled field from datasets (was unused)
  • Removed official field from datasets (community datasets are now detected by path prefix)
  • Removed deprecated and experimental fields from VirusProperties: compatibility, shortcuts, files, defaultCds, cdsOrderPreference

These changes simplify the schema and remove legacy fields that were no longer used. Dataset authors should remove these fields from their pathogen.json files.

Nextclade schemas: documentation improvements

Added doc comments and examples to JSON schema types, improving auto-completion and inline documentation in editors that support JSON Schema. Types with new documentation include:

  • Dataset index types (DatasetIndexJson, DatasetCollection, Dataset, DatasetVersion)
  • Output types (NextcladeOutputs, ResultsJson, NextcladeErrorOutputs)
  • QC config and result types
  • Tree and Auspice extension types
  • Gene and annotation types
  • Mutation and alignment types
  • Pathogen config and phenotype types
  • Alignment parameter types

Nextclade documentation

  • Fixed ref_nodes field types and added missing qry[].name field
  • Added missing fields to pathogen config documentation
  • Marked clade_node_attrs.displayName as required per schema
  • Corrected searchAlgo enum value from ancestor-latest to ancestor-nearest
  • Documented aaMutLabelMap (previously a TODO placeholder)
  • Fixed QC examples to use cdsName instead of geneName

Installation and usage

📚 Documentation: docs.nextstrain.org/projects/nextclade

🌍 Nextclade Web: clades.nextstrain.org

🖥️ Nextclade CLI:

  • 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures.
  • 🐋 Docker images are available on DockerHub
  • 🐍 Conda package is available in bioconda channel.

⌨️ Source code is on GitHub: github.com/nextstrain/nextclade

🚩 Report bugs, suggest features by submitting a GitHub issue

💾 Nextclade datasets are here
Assets 9
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