Write run time config to a file

This is generally useful for debugging and will be used by augur
subsample.

Note that while this is under the 'rules' folder, it is not a rule.
Instead, it is top-level workflow code run before rules to ensure that
the file is written on every workflow run, including dry runs.

Author: victorlin

CHANGELOG.md

@@ -4,6 +4,7 @@ We use this CHANGELOG to document breaking changes, new features, bug fixes, and
 
 ## 2025
 
+* 8 September 2025: Configuration resolved at run time is now written to a file under `results/run_configs`. [PR #102](https://github.com/nextstrain/WNV/pull/102) @victorlin
 * 8 September 2025: The phylogenetic workflow configuration now expects a new structure with most configuration defined under a build-specific key. See `phylogenetic/defaults/config.yaml` as an example. **This is a breaking change.** [PR #102](https://github.com/nextstrain/WNV/pull/102) @victorlin
 * 8 September 2025: The phylogenetic workflow now runs all Nextstrain-maintained builds by default. This can be adjusted by a new configuration option, `builds`. **This is a breaking change.** [PR #102](https://github.com/nextstrain/WNV/pull/102) @victorlin
 * 8 September 2025: Support for manual subsampling by editing the file `phylogenetic/rules/subsampling_manual.smk` is no longer supported. **This is a breaking change.** [PR #102](https://github.com/nextstrain/WNV/pull/102) @victorlin

phylogenetic/Snakefile

@@ -53,6 +53,7 @@ rule all:
 # custom_rules imported below to ensure that the core workflow is not complicated
 # by build specific rules.
 
+include: "rules/write_config.smk"
 include: "rules/merge_additional_inputs.smk"
 include: "rules/prepare_sequences.smk"
 include: "rules/subsample.smk"

phylogenetic/rules/write_config.smk

@@ -0,0 +1,21 @@
+"""
+This part of the workflow writes run time configuration to a YAML file.
+
+OUTPUTS:
+
+    results/run_configs/{timestamp}.yaml
+"""
+import os
+import sys
+import yaml
+from datetime import datetime
+
+timestamp = datetime.now().astimezone().strftime("%Y-%m-%dT%H%M%S.%f")
+path = f"results/run_configs/{timestamp}.yaml"
+
+os.makedirs(os.path.dirname(path), exist_ok=True)
+
+with open(path, 'w') as f:
+    yaml.dump(config, f, sort_keys=False)
+
+print(f"Saved current run config to {path!r}.", file=sys.stderr)