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 workflow can be run from the top level pathogen repo directory:
nextstrain build nextclade
Alternatively, the workflow can also be run from within the nextclade directory:
cd nextclade
nextstrain build .
This produces the default outputs of the nextclade workflow:
- nextclade_dataset(s) = datasets/<build_name>/*
The defaults 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 nextclade Snakefile succinct and organized.
The workdir is hardcoded to be the nextclade directory so all filepaths for
inputs/outputs should be relative to the nextclade directory.
Modules are all included in the main Snakefile in the order that they are expected to run.
The build-configs directory contains custom configs and rules that override and/or extend the default workflow.
- test-dataset - build to test new Nextclade dataset