From c10c777c135e9b596deed014778d975d6dc0a3a7 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Tue, 14 Oct 2025 13:34:48 -0700
Subject: [PATCH] Disable aliases in dumped config

Dumping the config with fully expanded contents is better for debugging
and potential reuse.

Workaround adapted from https://stackoverflow.com/a/66853182
---
 snakemake/config.smk | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/snakemake/config.smk b/snakemake/config.smk
index 15727b0..ada7c1c 100644
--- a/snakemake/config.smk
+++ b/snakemake/config.smk
@@ -156,6 +156,11 @@ def write_config(path):
     os.makedirs(os.path.dirname(path), exist_ok=True)
 
     with open(path, 'w') as f:
-        yaml.dump(config, f, sort_keys=False)
+        yaml.dump(config, f, sort_keys=False, Dumper=NoAliasDumper)
 
     print(f"Saved current run config to {path!r}.", file=sys.stderr)
+
+
+class NoAliasDumper(yaml.SafeDumper):
+    def ignore_aliases(self, data):
+        return True