Move phylogenetic workflow from top-level to folder phylogenetic

wip: use the experimental workflow from nextstrain/.github#57

wip

wip

Add general precommit lints

Add codespell to precommit

Add shellcheck to precommit

Add tomlsort to precommit

chore: lint/formatting

README.md

@@ -34,9 +34,3 @@ To activate pre-commit, run:
 ```bash
 pre-commit install
 ```
-
-## Development
-
-[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/nextstrain/monkeypox/master.svg)](https://results.pre-commit.ci/latest/github/nextstrain/monkeypox/master)
-
-This repository can be used with pre-commit to automatically run checks before committing.

nextclade/README.md

@@ -0,0 +1,44 @@
+# Nextclade reference tree workflow for monkeypox
+
+## Usage
+
+```bash
+snakemake
+```
+
+### Visualize results
+
+View results with:
+
+```bash
+nextstrain view auspice/
+```
+
+## Maintenance
+
+### Updating for new clades
+
+- [ ] Update each `config/{build}/clades.tsv` with new clades
+- [ ] Add new clades to color ordering
+- [ ] Check that clades look good, exclude problematic sequences as necessary
+
+### Creating a new dataset version
+
+Edit CHANGELOG.md
+
+## Configuration
+
+Builds differ in paths, relevant configs are pulled in through lookup.
+
+## Installation
+
+Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools.
+
+## Data use
+
+We gratefully acknowledge the authors, originating and submitting laboratories of the genetic
+sequences and metadata for sharing their work. Please note that although data generators have
+generously shared data in an open fashion, that does not mean there should be free license to
+publish on this data. Data generators should be cited where possible and collaborations should be
+sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if
+uncertain.