This workflow ingests public data from NCBI and outputs curated metadata and sequences that can be used as input for the phylogenetic workflow.
If you have another data source or private data that needs to be formatted for the phylogenetic workflow, then you can use a similar workflow to curate your own data.
The config directory contains all of the default configurations for the ingest workflow.
defaults/config.yaml contains all of the default configuration
parameters used for the ingest workflow. Use Snakemake's
--configfile/--config options to override these default values.
The rules directory contains separate Snakefiles (*.smk) as modules
of the core ingest 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.
This repository uses git subrepo to manage copies of ingest
scripts in vendored, from nextstrain/ingest
See vendored/README.md for instructions on how to update the vendored scripts.