CDCgov/phoenix

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🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens

Stars: 112
Forks: 41
Open beginner issues: 0
Indexed issues: 13

Dominant language: Python
License: Apache-2.0
Last GitHub push: Jul 2, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

Open All

13 open issues indexed

negative control auto-QC "pass" Open

Low Severity Bug: Universal

Difficulty 4/5 3-5 days Newbie friendliness 38/100

CDCgov/phoenix#225 · Opened Sep 15, 2026
[New Feature Request] - Simplify ShigaPass/FastANI taxonomy reconciliation logic Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

CDCgov/phoenix#223 · 1 comment · Opened Sep 3, 2026
Missing colon in collated_versions.yml with --create_ncbi_sheet flag Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

CDCgov/phoenix#221 · Opened Jul 24, 2026
Invalid workflow defniiton Open

CDCgov/phoenix#219 · 4 comments · 1 assignee · Opened Jul 1, 2026
Broken badge Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

CDCgov/phoenix#216 · Opened Jun 10, 2026
[BUG] ShigaPass field extraction pulls empty column Open

High Severity Bug: Universal

CDCgov/phoenix#215 · 4 comments · 1 assignee · Opened Jun 9, 2026
Optional Shovill-based assembly workflow Open

Enhancement

CDCgov/phoenix#203 · 2 comments · 1 assignee · Opened Apr 17, 2026
[New Feature Request] - Allow AWS S3 path for the CREATE_SRA_SAMPLESHEET function Open

Bug: System Specific Enhancement

CDCgov/phoenix#184 · 2 comments · 2 assignees · Opened Jan 27, 2025
Podman support - requested enhancement Open

Enhancement

CDCgov/phoenix#181 · 3 comments · 2 assignees · Opened Jan 22, 2025
Considering Bakta for genome annotation - requested enhancement Open

CDCgov/phoenix#177 · 1 comment · 1 assignee · Opened Dec 2, 2024
Create message/output when downstream and QC analysis is not complete or is interrupted due to taxa not assigned (taxa is not bacterial) Open

Enhancement

CDCgov/phoenix#123 · 1 comment · 1 assignee · Opened Oct 2, 2023
pigz error in PHOENIX:PHOENIX_EXTERNAL:ASSET_CHECK process on GCP VM Open

Bug: System Specific

CDCgov/phoenix#120 · 6 comments · 1 assignee · Opened Aug 18, 2023
Singe-end analysis - requested enhancement Open

Enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

CDCgov/phoenix#87 · 1 comment · Opened Feb 20, 2023

CDCgov/phoenix

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