This WNV Nextclade dataset was created guided by the Nextclade Dataset Creation Guide.
Previously, all "official" Nextclade workflows lived in a central GitHub repository. The new standard would be to include the Nextclade workflow within the pathogen repo.
This workflow is used to create the Nextclade datasets for this pathogen. All official Nextclade datasets are available at https://github.com/nextstrain/nextclade_data.
The config directory contains all of the default configurations for the Nextclade workflow.
defaults/config.yaml contains all of the default configuration parameters
used for the Nextclade workflow. Use Snakemake's --configfile/--config
options to override these default values.
The rules directory contains separate Snakefiles (*.smk) as modules of the core Nextclade workflow.
The modules of the workflow are in separate files to keep the main ingest Snakefile succinct and organized.
Modules are all included
in the main Snakefile in the order that they are expected to run.