Pipeline Prototype v0.5.0

Changes since v0.4.0

• Add initialisation only workflow
• Update README.md on how to use initialisation only workflow

Full Changelog: v0.4.0-alpha...v0.5.0-alpha

Pipeline Prototype v0.4.0 (basic features complete)

Changes since v0.3.0

• Basic features completed. All fundamental modules in place.
• Include AMRsearch to infer other AMR
• Unify output values of PBP AMR and other AMR
• Update README.md for other AMR

Full Changelog: v0.3.0-alpha...v0.4.0-alpha

Dockerised Pipeline Prototype v0.3.0

Changes since v0.2.1

• Include CDC PBP AMR Predictor to provide AMR prediction related to pbp genes
• Improve offline capability
• Better support for common FASTQ naming conventions
• Improve README.md
  • Improve description
  • Add credits for all open-source components
  • Add details about the output summary.csv file

Full Changelog: v0.2.1-alpha...v0.3.0-alpha

Dockerised Pipeline Prototype v0.2.1

A working prototype of the GPS Unified Pipeline

• The pipeline now runs fully in Docker environments
• In silico AMR prediction is not yet implemented

v0.2.1 Hotfix

• Prevent permission issue with LINEAGE module

Dockerised Pipeline Prototype v0.2

A working prototype of the GPS Unified Pipeline

• The pipeline now runs fully in Docker environments
• In silico AMR prediction is not yet implemented

Predocker Pipeline Prototype v0.1

A working prototype of the GPS Unified Pipeline

• The environments are not fully dockerised
• In silico AMR prediction is not yet implemented