Issues · nextstrain/pathogen-repo-guide · GitHub

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ingest: Add summary QC columns `QC_overall_score` and `QC_overall_status` to defaults

#103

· j23414 opened

on Feb 2, 2026

Document what "compatible with nextstrain run" means

#102

· joverlee521 opened

on Jan 28, 2026

Simplify `params.current_basedir`

#99

· victorlin opened

on Oct 15, 2025

Support dynamic CLI calls through config centralization

#98

· victorlin opened

on Oct 3, 2025

Define a schema for workflow config files

#95

· victorlin opened

on Sep 24, 2025

Move `docs/nextstrain-internal`

#92

· joverlee521 opened

on Sep 15, 2025

Add workaround for NCBI Datasets' incompatibility issues

#82

· joverlee521 opened

on Feb 24, 2025

Standardized composable configs

#79

· joverlee521 opened

on Dec 10, 2024

work needed to allow users to run analyses separate to pathogen workflows

#74

· jameshadfield opened

on Nov 24, 2024

Bacterial workflow support

#64

· genehack opened

on Oct 2, 2024

ingest: Add standardized steps for curating host

#63

· joverlee521 opened

on Aug 20, 2024

ingest: How to handle segmented viruses

#59

· joverlee521 opened

on Jul 26, 2024