Update README [#2]

README.md

@@ -1,36 +1,61 @@
 # Nextstrain repository for yellow fever virus
 
-<!-- ##TODO## finish updating this -->
+This repository contains three workflows for the analysis of yellow
+fever virus data:
 
-This repository is in the process of being upgraded to follow the
-[pathogen repo guide][].
+- [`ingest/`] - Download data from GenBank, clean and curate it
+- [`phylogenetic/`][] - Filter sequences, align, construct phylogeny,
+  and export for visualization
+- [`nextclade/`][] - Create nextclade datasets
+
+Each workflow directory contains a `README.md` file with more
+information. The results of running both workflows are publicly
+visible at [nextstrain.org/yellow-fever][].
 
 ## Installation
 
 Follow the [standard installation instructions][] for Nextstrain's
 suite of software tools.
 
-## Working on this repo
+## Quick start
+
+Run the phylogenetic workflow by executing the following commands in
+the repository checkout, after installing `nextstrain` per the above
+instructions:
+
+```bash
+cd phylogenetic/
+nextstrain build .
+nextstrain view .
+```
+
+Further documentation is available at "[Running a pathogen workflow][]".
+
+## Working on this repository
 
-This repo is configured to use [pre-commit][] to help automatically
-catch common coding errors and syntax issues with changes before they
-are committed to the repo.
+This repository is configured to use [pre-commit][] to help
+automatically catch common coding errors and syntax issues with
+changes before they are committed to the repo.
 
-If you will be writing new code or otherwise working within this repo,
-please do the following to get started:
+If you will be writing new code or otherwise working within this
+repository, please do the following to get started:
 
-1. install `pre-commit` by running either `python -m pip install
+1. install `pre-commit`, by running either `python -m pip install
    pre-commit` or `brew install pre-commit`, depending on your
    preferred package management solution
 2. install the local git hooks by running `pre-commit install` from
-   the root of the repo
+   the root of the repository
 3. when problems are detected, correct them in your local working tree
    before committing them.
 
 Note that these pre-commit checks are also run in a GitHub Action when
 changes are pushed to GitHub, so correcting issues locally will
 prevent extra cycles of correction.
 
-[pathogen repo guide]: https://github.com/nextstrain/pathogen-repo-guide/
+[`ingest/`]: ./ingest
+[`phylogenetic/`]: ./phylogenetic
+[`nextclade/`]: ./nextclade
+[nextstrain.org/yellow-fever]: https://nextstrain.org/yellow-fever
+[Running a pathogen workflow]: https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html
 [pre-commit]: https://pre-commit.com
 [standard installation instructions]: https://docs.nextstrain.org/en/latest/install.html