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@nextstrain-bot nextstrain-bot released this 19 Jun 07:12
3.7.2
cf1eb54

Nextclade 3.7.2

General

[fix] Avoid duplicate node names in the output Auspice JSON tree

When multiple query samples were to be placed onto the same node on the reference tree, sometimes multiple auxiliary nodes could be created having the same name. Node names are expected to be unique for Auspice visualization to work correctly, so when visualizing the tree Auspice have been renaming these nodes and emitting warnings into browsers' dev console.

In this version we pick unique names for the auxiliary nodes during placement, so that there are no more warnings. Users may observe changes in some of the node names when inspecting output Auspice JSON file. However, this unlikely to affect most users' work.

Nextclade Web

[fix] Ensure dataset "updated at" date is displayed in Nextclade Web

Since 3.7.0 Nextclade Web is not showing "updated at" date for any datasets. This has been fixed.

[fix] Ensure frame shift and insertion markers in sequence views can also be toggled

Most markers can be toggled on or off on the sequence views in "Settings" page in Nextclade Web, however frame shifts and insertions could not be. We added the missing toggles.

[fix] Correctly style details/summary component

The text in details/summary ("collapse", "spoiler") component (e.g. the list of SC2 lineages) overflowing and producing garbled text in dataset readmes and changelogs. This has been fixed.

[dep] Update Auspice tree visualization to 2.55.0

Auspice tree visualization package has been updated from 2.53.0 to 2.55.0. See Auspice changelog here.

Internal

[infra] Fix feature-policy and permission-policy HTTP headers

The deprecated feature-policy header was removed entirely and interest-cohort entry was removed from the permission-policy header. Latest versions of web browsers should no longer emit warnings into console.

[test] Test Nextclade CLI on more Linx distros

Additionally to the previous, we now test Nextclade CLI on the following newer Linux distributions:

  • Amazon Linux 2.0.2024
  • Debian 12
  • Fedora 41
  • Oracle Linux 8.9
  • Ubuntu 24.04

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.
Assets 9
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