Writing Custom Scripts

This tutorial bridges the gap between running standard shell commands and writing complex logic within oxo-flow. Often, a single shell command isn't enough to process bioinformatics data, and you'll need to embed Python, R, or Bash scripts directly into your workflow.

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The script Directive

oxo-flow provides a clean way to execute inline or external scripts while still benefiting from dependency tracking and environment isolation.

(Tutorial content is currently under development as part of Milestone 9.6. Please check back soon or consult the Command Reference in the meantime.)