Glossary

analysis directory

The folder within ncov/ where customization files live. Previously this was my_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 config file, workflow configuration file, builds.yaml

A YAML file used to configure the Snakemake workflow (via the --configfile option). Appends to and overrides default configuration in defaults/parameters.yaml. For the ncov workflow, this file must follow a specific format.

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.