geniac’s documentation!

Geniac: Automatic Configuration GENerator and Installer for nextflow pipeline.

Contents:

• Introduction
  • Context
  • Resources
  • Acknowledgements
  • Citation
• Get started
  • Prerequisites
  • Start a new repository
  • Naming convention
• Add a process
  • Structure of a process
  • Answer these questions first
  • Guidelines
  • Results
• Check the code
  • Install the geniac linter
  • Launch the geniac linter
• Installation
  • Configure
  • Containers
  • Custom targets
  • Structure of the installation directory tree
  • Examples
• Development cycle
  • Prototyping
  • Containerizing
  • Deployment
  • Git
• Run the pipeline
  • Profiles
  • Options
  • Results
  • Examples
• Admin
  • Structure of the build directory tree
  • Generate preload cache with default values
  • Containers
• FAQ
  • How can I use geniac on an existing repository?
  • How does the repository look like?
  • How can I write the config files for the different nextflow profiles?
  • How should I define the path to the genome annotations?
  • How can I pass specific options to run docker or singularity containers?
  • How can I see the recipes for the containers?
  • Is geniac compatible with nextflow DSL2?
  • What are the @git_*@ variables?
  • Why the conda profile fails to build its environment or takes to much time?