WIP export segment specific metadata

This adds back in segment-specific metadata to the Auspice JSON. There
are multiple ways this can be done, each with trade-offs. The approach
employed here leaves the "_{segment}" suffix on the field names.
Alternatively we could remap the metadata file for each `export` call so
that (e.g.) "accession_S" becomes "accession".

phylogenetic/defaults/auspice_config.json

@@ -50,8 +50,5 @@
     "host",
     "region",
     "abbr_authors"
-  ],
-  "metadata_columns": [
-    "accession"
   ]
 }

phylogenetic/defaults/config.yaml

@@ -35,3 +35,9 @@ traits:
 export:
   auspice_config: "defaults/auspice_config.json"
   description: "defaults/description.md"
+  segment_metadata_columns:
+    - accession_{segment}
+    - qc_{segment}
+    - length_{segment}
+    - date_released_{segment}
+    - date_updated_{segment}

phylogenetic/rules/export.smk

@@ -56,6 +56,7 @@ rule export:
         auspice = "auspice/oropouche_{segment}.json",
     params:
         strain_id_field = config["strain_id_field"],
+        metadata_columns = lambda w: [name.format(segment=w.segment) for name in config["export"]["segment_metadata_columns"]]
     shell:
         """
         augur export v2 \
@@ -66,6 +67,7 @@ rule export:
             --description {input.description} \
             --colors {input.colors} \
             --auspice-config {input.auspice_config} \
+            --metadata-columns {params.metadata_columns} \
             --output {output.auspice} \
             --include-root-sequence-inline
         """