Building one pipeline is straightforward. Building three that share infrastructure without duplicating bugs is a different problem entirely. This is why I built OmniDomain.
After finishing NextAMR, I’m expanding to fungi and plants. OmniDomain is a unified Nextflow + AWS Batch platform for bacterial, fungal, and plant genomics — one shared infrastructure, three pipeline engines.
The core idea: fix a memory bug once, all pipelines inherit it.
Current status:
- 🦠 NextAMR bacterial WGS + AMR detection (published)
- 🍄 FungalFlow fungal assembly + BGC detection (building)
- 🌱 PhytoFlow plant HiFi assembly + annotation (architecting)
- 🧬 Metacflow bacterial metagenomics (v2.0)