Further updates to READMEs

1. Installation section in top-level readme (I'm always looking for this)
2. Make it clearer that phylogenetic workflow needs to be run from within the phylogenetic/ directory

README.md

@@ -3,15 +3,17 @@
 This repository contains two workflows for the analysis of Zika virus data:
 
 - [`ingest/`](./ingest) - Download data from GenBank, clean and curate it and upload it to S3
-- [`phylogenetic/`](./phylogenetic) - Make phylogenetic trees for nextstrain.org
+- [`phylogenetic/`](./phylogenetic) - Filter sequences, align, construct phylogeny and export for visualization
 
-Each folder contains a README.md with more information.
+Each folder contains a README.md with more information. The results of running both workflows are publicly visible at [nextstrain.org/zika](https://nextstrain.org/zika).
 
-## Quickstart
+## Installation
+
+Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools.
 
-Follow the [standard installation instructions](https://docs.nextstrain.org/page/install.html) for Nextstrain's suite of software tools.
+## Quickstart
 
-Then run the default phylogenetic workflow via:
+Run the default phylogenetic workflow via:
 ```
 cd phylogenetic/
 nextstrain build .
@@ -20,4 +22,5 @@ nextstrain view .
 
 ## Documentation
 
+- [Running a pathogen workflow](https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html)
 - [Contributor documentation](./CONTRIBUTING.md)

phylogenetic/README.md

@@ -5,38 +5,42 @@ This is the [Nextstrain](https://nextstrain.org) build for Zika, visible at
 
 ## Software requirements
 
-Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools.
+Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html)
+for Nextstrain's suite of software tools.
 
 ## Usage
 
 If you're unfamiliar with Nextstrain builds, you may want to follow our
 [Running a Pathogen Workflow guide][] first and then come back here.
 
 The easiest way to run this pathogen build is using the Nextstrain
-command-line tool:
+command-line tool from within the `phylogenetic/` directory:
 
+    cd phylogenetic/
     nextstrain build .
 
 Build output goes into the directories `data/`, `results/` and `auspice/`.
 
-Once you've run the build, you can view the results in auspice:
+Once you've run the build, you can view the results with:
 
-    nextstrain view auspice/
+    nextstrain view .
 
 ## Configuration
 
-Configuration takes place entirely with the `Snakefile`. This can be read top-to-bottom, each rule
-specifies its file inputs and output and also its parameters. There is little redirection and each
-rule should be able to be reasoned with on its own.
+Configuration takes place entirely with the `Snakefile`. This can be read
+top-to-bottom, each rule specifies its file inputs and output and also its
+parameters. There is little redirection and each rule should be able to be
+reasoned with on its own.
 
 ### Using GenBank data
 
-This build starts by pulling preprocessed sequence and metadata files from: 
+This build starts by pulling preprocessed sequence and metadata files from:
 
 * https://data.nextstrain.org/files/zika/sequences.fasta.zst
 * https://data.nextstrain.org/files/zika/metadata.tsv.zst
 
-The above datasets have been preprocessed and cleaned from GenBank and are updated at regular intervals.
+The above datasets have been preprocessed and cleaned from GenBank using the
+[ingest/](../ingest/) workflow and are updated at regular intervals.
 
 ### Using example data