Developers
This section provides detailed reference documentation for the individual components that make up Bactopia workflows.
CLI Reference
Full command-line reference for all Bactopia commands and their options.
nf-bactopia Plugin
Developer reference for the nf-bactopia Nextflow plugin -- utility functions and operators used across Bactopia workflows.
AI Skills
Automation skills that orchestrate Bactopia CLI commands through AI-assisted coding tools for scaffolding, maintenance, review, and testing tasks. There are 12 skills available.
Subworkflows
Subworkflows orchestrate multiple modules into reusable analysis units. There are 86 subworkflows available.
Modules
Modules are individual processes that perform specific analysis tasks. There are 97 modules available.