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Snakemake 8.1.1 documentation

Getting started

  • Installation
  • Migration between Snakemake versions
  • Best practices
  • Snakemake Tutorial

Executing workflows

  • Command line interface
  • Job Grouping
  • Between workflow caching
  • Interoperability
  • Monitoring

Defining workflows

  • Writing Workflows
  • Snakefiles and Rules
  • Configuration
  • Modularization
  • Storage support
  • Utils
  • Distribution and Reproducibility
  • Reports
  • Automatically generating unit tests
  • Integrating foreign workflow management systems

Project Info

  • Citing and Citations
  • More Resources
  • Frequently Asked Questions
  • Contributing
  • Credits
  • Changelog
  • License
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