Merge pull request #120: Update example data

Author: victorlin

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 We use this CHANGELOG to document breaking changes, new features, bug fixes, and config value changes that may affect both the usage of the workflows and the outputs of the workflows.
 
+## 2026
+
+* 9 March 2026: Added date annotations to some sequences from 1998 and 1999. [PR #120](https://github.com/nextstrain/WNV/pull/120) @victorlin
+
 ## 2025
 
 * 25 February 2026: Changes to files referenced in `subsample` config will trigger a re-run of the rule. [PR #116](https://github.com/nextstrain/WNV/pull/116) @victorlin

ingest/defaults/annotations.tsv

@@ -17,6 +17,11 @@ EF631123	date	XXXX-XX-XX
 DQ116961	date	2004-XX-XX
 AY603654	date	1976-XX-XX
 AM404308	date	1971-XX-XX
-AF260968	date	1951-XX-XX
 AY660002	date	2003-XX-XX
 AY268132	date	2000-XX-XX
+AF202541	date	1999-XX-XX
+AF206518	date	1999-XX-XX
+AF481864	date	1998-XX-XX
+AY277251	date	1998-XX-XX
+NC_001563	date	1937-XX-XX
+NC_009942	date	1999-XX-XX

phylogenetic/README.md

@@ -38,7 +38,7 @@ Any desired data formatting and curations should be done as part of the [ingest]
 
 The first step in the phylogenetic workflow is to subsample (or filter) the data. The subsampling criteria are specified in the 
 phylogenetic/config/defaults.yaml file. The criteria are then executed in the Snakefile using wildcards and an input function. 
-Documentation about subsampling can be found here [filtering and subsampling] (https://docs.nextstrain.org/en/latest/guides/bioinformatics/filtering-and-subsampling.html#subsampling-within-augur-filter)
+Documentation about subsampling can be found here [filtering and subsampling](https://docs.nextstrain.org/en/latest/guides/bioinformatics/filtering-and-subsampling.html#subsampling-within-augur-filter)
 
 
 ## Defaults
@@ -65,6 +65,18 @@ in the main Snakefile in the order that they are expected to run.
 The build-configs directory contains custom configs and rules that override and/or
 extend the default workflow.
 
-- [ci](build-configs/ci/) - CI build that runs with example data
+- [chores](build-configs/chores/) - chores that are run separately from the main workflow
+- [ci](build-configs/ci/) - [CI][] build that runs with [example data][]
 
+## Update example data
+
+[example data][] should be updated occasionally. To update, run:
+
+```bash
+nextstrain build . update_example_data -F \
+    --configfiles defaults/config.yaml build-configs/chores/config.yaml
+```
+
+[CI]: https://github.com/nextstrain/WNV/actions/workflows/ci.yaml
+[example data]: ./example_data/
 [Nextstrain datasets]: https://docs.nextstrain.org/en/latest/reference/glossary.html#term-dataset

phylogenetic/build-configs/chores/chores.smk

@@ -0,0 +1,29 @@
+rule update_example_data:
+    """This updates the files under example_data/ based on latest available data from data.nextstrain.org.
+
+    The subset of data is generated by an augur filter call which:
+    - sets the subsampling size to 50
+    - samples evenly across time
+    - adds everything in defaults/all-lineages/include.txt
+    """
+    input:
+        sequences="results/sequences.fasta",
+        metadata="results/metadata.tsv",
+    output:
+        sequences="example_data/sequences.fasta",
+        metadata="example_data/metadata.tsv",
+    params:
+        strain_id=config["strain_id_field"],
+    shell:
+        r"""
+        augur filter \
+            --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
+            --sequences {input.sequences} \
+            --subsample-max-sequences 50 \
+            --group-by month \
+            --subsample-seed 0 \
+            --include defaults/all-lineages/include.txt \
+            --output-metadata {output.metadata} \
+            --output-sequences {output.sequences}
+        """

phylogenetic/build-configs/chores/config.yaml

@@ -0,0 +1,2 @@
+custom_rules:
+  - build-configs/chores/chores.smk