geniac’s documentation!

Geniac: Automatic Configuration GENerator and Installer for nextflow pipelines.

Contents:

• Introduction
  • Context
  • Resources
  • Acknowledgements
  • Cite us
• Get started
  • Prerequisites
  • Test geniac on the geniac-demo pipeline
  • Start a new repository
  • Naming convention
• Add a process
  • Structure of a process
  • Answer these questions first
  • Guidelines
  • Results
• Check the code
• 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
• Geniac CLI
  • Install the geniac command line interface
  • Initiate a geniac working directory
  • Check the code with the geniac linter
  • Install the pipeline with the singularity images
  • Install the pipeline using existing singularity images
  • Generate the configuration files
  • Generate the container recipes
  • Test the pipeline with the singularity profile
  • Test the pipeline with the singularity and cluster profiles
  • Clean the geniac work directory
  • List available cmake options
• Admin
  • Structure of the build directory tree
  • Generate preload cache with default values
  • Containers
  • Documentation
• FAQ
  • How can I use geniac on an existing repository?
  • How does the repository look like?
  • How can I install custom commands in the docker/singularity recipes automatically generated by geniac?
  • How can I use a custom docker registry to build the containers?
  • 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 a conda environment be activated in docker or singularity containers?
  • How can I see the recipes for the containers?
  • How can I generate all the files automatically created by geniac without installing the pipeline?
  • Is geniac compatible with nextflow DSL2?
  • How can a process have a label which is defined by a variable?
  • What are the @git_*@ variables?
  • Why does the conda profile fail to build its environment or take to much time?
  • Why are the tools available from source installed in pipeline/bin/fromSource and not in pipeline/bin?
  • What privileges do I need to build the singularity images?
  • What is the difference between singularity and apptainer?
• Miscellaneous
  • Add custom commands and environment variables in the docker/singularity recipes automatically generated by geniac
  • How can a conda environment be activated in docker or singularity containers?
  • Linux distributions used for the containers
  • Config files for the different nextflow profiles
  • Install tools from source: more examples
  • R with reproducible environments using renv package