Merge pull request #12: Update top-level name

.github/workflows/ci.yaml

@@ -8,4 +8,4 @@ jobs:
   ci:
     uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master
     with:
-      build-args: auspice/flu_avian_h5n1_ha.json
+      build-args: auspice/avian-flu_h5n1_ha.json

batch.py

@@ -30,8 +30,8 @@
         for segment in params.segments:
             call = ['nextstrain', 'build', '--aws-batch', '.', '-j 1']
             targets = []
-            targets.append('auspice/flu_avian_%s_%s_tree.json'%(subtype, segment))
-            targets.append('auspice/flu_avian_%s_%s_meta.json'%(subtype, segment))
+            targets.append('auspice/avian-flu_%s_%s_tree.json'%(subtype, segment))
+            targets.append('auspice/avian-flu_%s_%s_meta.json'%(subtype, segment))
             call.extend(targets)
             print(' '.join(call))
             log = open('logs/%s_%s.txt'%(subtype, segment), 'w')

quickstart-build/Snakefile

@@ -15,7 +15,7 @@ SEGMENTS = ["ha"]
 generated JSON files in the auspice folder for each subtype and segment."""
 rule all:
     input:
-        auspice_json = expand("auspice/flu_avian_{subtype}_{segment}.json", subtype=SUBTYPES, segment=SEGMENTS)
+        auspice_json = expand("auspice/avian-flu_{subtype}_{segment}.json", subtype=SUBTYPES, segment=SEGMENTS)
 
 """Specify all input files here. For this build, you'll start with input sequences
 from the example_data folder, which contain metadata information in the
@@ -305,7 +305,7 @@ rule export:
         node_data = node_data_by_wildcards,
         auspice_config = files.auspice_config
     output:
-        auspice_json = "auspice/flu_avian_{subtype}_{segment}.json"
+        auspice_json = "auspice/avian-flu_{subtype}_{segment}.json"
     shell:
         """
         augur export v2 \