phylogenetic: Add root-sequence.json to rule all

Explicitly state that the root-sequence.json file is an expected output
of the core phylogenetic workflow.

This also ensures that the Nextstrain automation rule `deploy_all`
will include the root-sequence.json in the upload.

phylogenetic/Snakefile

@@ -1,10 +1,13 @@
 genes = ['N450', 'genome']
 
-configfile: "defaults/config.yaml" 
+configfile: "defaults/config.yaml"
 
 rule all:
     input:
-        auspice_json = expand("auspice/measles_{gene}.json", gene=genes)
+        expand([
+            "auspice/measles_{gene}.json",
+            "auspice/measles_{gene}_root-sequence.json"
+        ], gene=genes)
 
 include: "rules/prepare_sequences.smk"
 include: "rules/prepare_sequences_N450.smk"