Glossary
- analysis directory
The folder within
ncov/
where customization files live. Previously this wasmy_profiles/
but we now allow any name of choice, and provide ncov-tutorial as a starter template.- Auspice config file
also
auspice_config.json
A JSON file used to configure visualization in Auspice.
- config file
also workflow configuration file,
builds.yaml
A YAML file used for Snakemake’s
--configfile
parameter. Appends to and overrides default configuration indefaults/parameters.yaml
.- customization file
A file used to customize the ncov workflow.
Examples: Auspice config file, workflow config file, default files
- default files
Default customization files provided in
ncov/defaults/
.- ncov workflow
also SARS-CoV-2 workflow
The workflow used to automate execution of builds. Implemented in Snakemake.
- Snakemake
The workflow manager used in the ncov workflow.