fix: flag output directory with directory()

Resolves error:

```
ImproperOutputException in rule prepare_nextclade in file /home/runner/work/ncov/ncov/workflow/snakemake_rules/main_workflow.smk, line 452:
Outputs of incorrect type (directories when expecting files or vice versa). Output directories must be flagged with directory(). for rule prepare_nextclade:
    output: data/sars-cov-2-nextclade-defaults
    affected files:
        data/sars-cov-2-nextclade-defaults
```

https://github.com/nextstrain/ncov/actions/runs/13007476969/job/36277462988?pr=1170#step:8:136

workflow/snakemake_rules/main_workflow.smk

@@ -455,7 +455,7 @@ rule prepare_nextclade:
         Downloading reference files for nextclade (used for alignment and qc).
         """
     output:
-        nextclade_dataset = "data/sars-cov-2-nextclade-defaults",
+        nextclade_dataset = directory("data/sars-cov-2-nextclade-defaults"),
     params:
         name = config["nextclade_dataset"],
     conda: config["conda_environment"]