# Ingest workflow for rubella virus

This workflow ingests public data from NCBI and outputs curated
metadata and sequences that can be used as input for the rubella
`nextclade` and `phylogenetic` workflows.

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.

## Config

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.

## Snakefile and rules

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.

## Vendored

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.

[defaults/config.yaml]: ./config/defaults.yaml
[`git subrepo`]: https://github.com/ingydotnet/git-subrepo
[included]: https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#includes
[nextstrain/ingest]: https://github.com/nextstrain/ingest
[Snakefile]: ./Snakefile
[vendored]: ./vendored
[vendored/README.md]: ./vendored/README.md#vendoring
