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Contents:

  • Introduction
  • Get started
  • Add a process
  • Check the code
  • Installation
  • Development cycle
  • Run the pipeline
  • Admin
  • FAQ
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  • geniac’s documentation!
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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?
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© Copyright 2019-2021, Philippe Hupé Revision 3efe35d6.

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