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Update workflows for Snakemake v9.16.3

Status: Open.

#37 In nextstrain/public;

· victorlin opened on Feb 11, 2026

pathogens: Update PPX builds to use OPEN data in default config

Status: Open.

#36 In nextstrain/public;

· joverlee521 opened on Feb 5, 2026

Add epitope coloring for existing pathogens

Status: Open.

#35 In nextstrain/public;

· joverlee521 opened on Feb 3, 2026

Enforce hierarchy in clade assignments

Status: Open.

#34 In nextstrain/public;

· joverlee521 opened on Dec 24, 2025

Output filter/subsample log

Status: Open.

#33 In nextstrain/public;

· joverlee521 opened on Dec 4, 2025

Add geographic streamtrees support to relevant pathogens

Status: Open.

#32 In nextstrain/public;

· joverlee521 opened on Dec 1, 2025

Replace assign-colors.py

Status: Open.

#30 In nextstrain/public;

· joverlee521 opened on Oct 21, 2025

Use Pathoplexus

Status: Open.

#29 In nextstrain/public;

· victorlin opened on Oct 17, 2025

Use augur subsample

Status: Open.

#26 In nextstrain/public;

· victorlin opened on Sep 25, 2025

Add/update multiple input support for existing pathogens

Status: Open.

#25 In nextstrain/public;

· joverlee521 opened on Sep 23, 2025

Output filtered metadata

Status: Open.

#24 In nextstrain/public;

· victorlin opened on Sep 15, 2025

Add/update CHANGELOG for existing pathogens

Status: Open.

#22 In nextstrain/public;

· joverlee521 opened on Jun 16, 2025