Issues

• negative control auto-QC "pass"

  Low Severity Bug: Universal
  CDCgov/phoenix#225 · Filter by author janis0616 opened on Sep 15, 2026
  1

• [New Feature Request] - Simplify ShigaPass/FastANI taxonomy reconciliation logic

  CDCgov/phoenix#223 · Filter by author weichisyu opened on Sep 3, 2026
  1

• Invalid workflow defniiton

  CDCgov/phoenix#219 · Filter by author DNA-Bioboss opened on Jul 1, 2026
  4

  

• Broken badge

  CDCgov/phoenix#216 · Filter by author tseemann opened on Jun 10, 2026

• [BUG] ShigaPass field extraction pulls empty column

  High Severity Bug: Universal
  CDCgov/phoenix#215 · Filter by author hutchinsonmiri opened on Jun 9, 2026
  4

  

• Optional Shovill-based assembly workflow

  Enhancement
  CDCgov/phoenix#203 · Filter by author vascokarla opened on Apr 17, 2026
  2

  

• [New Feature Request] - Allow AWS S3 path for the CREATE_SRA_SAMPLESHEET function

  Bug: System SpecificEnhancement
  CDCgov/phoenix#184 · Filter by author vitu1 opened on Jan 27, 2025
  2

  

• Podman support - requested enhancement

  Enhancement
  CDCgov/phoenix#181 · Filter by author jvhagey opened on Jan 22, 2025
  3

  

• Considering Bakta for genome annotation - requested enhancement

  CDCgov/phoenix#177 · Filter by author vascokarla opened on Dec 2, 2024
  1

  

• Create message/output when downstream and QC analysis is not complete or is interrupted due to taxa not assigned (taxa is not bacterial)

  Enhancement
  CDCgov/phoenix#123 · Filter by author MOREYCK opened on Oct 2, 2023
  1

  

• pigz error in PHOENIX:PHOENIX_EXTERNAL:ASSET_CHECK process on GCP VM

  Bug: System Specific
  CDCgov/phoenix#120 · Filter by author kprus opened on Aug 18, 2023
  6

  

• Singe-end analysis - requested enhancement

  Enhancement
  CDCgov/phoenix#87 · Filter by author AroobAlhumaidy opened on Feb 20, 2023
  1