Merge pull request #183 from nextstrain/upload-all-segment-sequences

Upload sequences for all segments to S3

profiles/upload.yaml

@@ -51,6 +51,12 @@ lat-longs: "config/lat_longs.tsv"
 segments:
   - ha
   - na
+  - pb2
+  - pb1
+  - pa
+  - np
+  - mp
+  - ns
 
 tree:
   method: iqtree
@@ -206,37 +212,3 @@ builds:
       - name: vidrl_ferret_egg_hi
         data: "data/vic/vidrl_ferret_egg_hi_titers.tsv"
     subsamples: *representative-subsampling-scheme
-  yam_2y:
-    lineage: yam
-    reference: "config/yam/{segment}/reference.fasta"
-    annotation: "config/yam/{segment}/genemap.gff"
-    tree_exclude_sites: "config/yam/{segment}/exclude-sites.txt"
-    clades: "config/yam/ha/clades.tsv"
-    auspice_config: "config/yam/auspice_config.json"
-    min_date: "2Y"
-    reference_min_date: "8Y"
-    include: "config/yam/reference_strains.txt"
-    exclude: "config/yam/outliers.txt"
-    vaccines: "config/yam/vaccine.json"
-    titer_collections:
-      - name: who_ferret_cell_hi
-        data: "data/yam/who_ferret_cell_hi_titers.tsv"
-      - name: who_ferret_egg_hi
-        data: "data/yam/who_ferret_egg_hi_titers.tsv"
-      - name: cdc_ferret_cell_hi
-        data: "data/yam/cdc_ferret_cell_hi_titers.tsv"
-      - name: cdc_ferret_egg_hi
-        data: "data/yam/cdc_ferret_egg_hi_titers.tsv"
-      - name: crick_ferret_cell_hi
-        data: "data/yam/crick_ferret_cell_hi_titers.tsv"
-      - name: crick_ferret_egg_hi
-        data: "data/yam/crick_ferret_egg_hi_titers.tsv"
-      - name: niid_ferret_cell_hi
-        data: "data/yam/niid_ferret_cell_hi_titers.tsv"
-      - name: niid_ferret_egg_hi
-        data: "data/yam/niid_ferret_egg_hi_titers.tsv"
-      - name: vidrl_ferret_cell_hi
-        data: "data/yam/vidrl_ferret_cell_hi_titers.tsv"
-      - name: vidrl_ferret_egg_hi
-        data: "data/yam/vidrl_ferret_egg_hi_titers.tsv"
-    subsamples: *representative-subsampling-scheme