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augur subsample: merging of external & default configs

Status: Open.

#106 In nextstrain/rsv;

· victorlin opened on Sep 23, 2025

Use augur subsample

enhancementNew feature or requestNew feature or request

Status: Open.

#101 In nextstrain/rsv;

· victorlin opened on Sep 22, 2025

phylo: drop rule rename_and_ready_for_nextclade

Status: Open.

#96 In nextstrain/rsv;

· jameshadfield opened on Aug 11, 2025

phylo: Replace <code>set_final_strain_name.py</code>

enhancementNew feature or requestNew feature or request

Status: Open.

#95 In nextstrain/rsv;

· joverlee521 opened on Aug 11, 2025

IQtree failed the past 2 rebuild attempts with "Some sequences (see above) are problematic, please check your alignment again"

bugSomething isn't workingSomething isn't working

Status: Open.

#79 In nextstrain/rsv;

· corneliusroemer opened on Mar 31, 2025

Update repo structure to match pathogen-repo-guide

source: office hoursIssue mentioned during office hoursIssue mentioned during office hours

Status: Open.

#77 In nextstrain/rsv;

· joverlee521 opened on Mar 13, 2025

Properly handle CSV-like TSVs

Status: Open.

#74 In nextstrain/rsv;

· joverlee521 opened on Dec 6, 2024

Rename <code>master</code> to <code>main</code>

enhancementNew feature or requestNew feature or request

Status: Open.

#63 In nextstrain/rsv;

· genehack opened on Jun 11, 2024

Add --start and --end flags to newreferences.py to allow for creating subgenic tree builds

enhancementNew feature or requestNew feature or request

Status: Open.

#56 In nextstrain/rsv;

· j23414 opened on Mar 12, 2024

Add detailed usage docs

documentationImprovements or additions to documentationImprovements or additions to documentation

source: office hoursIssue mentioned during office hoursIssue mentioned during office hours

Status: Open.

#44 In nextstrain/rsv;

· joverlee521 opened on Oct 26, 2023