Pull in changes from master into 2y branch

This commit pulls in changes on master branch that were not present on 2y branch
nextstrain · Apr 23, 2024 · 7549b7d · 7549b7d
1 parent 1ebb5ea
commit 7549b7d
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Showing 8 changed files with 184 additions and 11 deletions.
diff --git a/.github/workflows/ci.yaml b/.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_all-time.json
+      build-args: auspice/avian-flu_h5n1_ha_all-time.json
diff --git a/Snakefile b/Snakefile
@@ -7,16 +7,13 @@ path_to_fauna = '../fauna'
 
 def all_targets():
     return [
-        *expand("auspice/flu_avian_{subtype}_{segment}_{time}.json", subtype=["h5nx","h5n1"], segment=SEGMENTS,time=TIME),
-        *expand("auspice/flu_avian_{subtype}_{segment}_{time}.json", subtype=['h7n9', 'h9n2'], segment=SEGMENTS,time=['all-time'])
+        *expand("auspice/avian-flu_{subtype}_{segment}_{time}.json", subtype=["h5nx","h5n1"], segment=SEGMENTS,time=TIME),
+        *expand("auspice/avian-flu_{subtype}_{segment}_{time}.json", subtype=['h7n9', 'h9n2'], segment=SEGMENTS,time=['all-time'])
     ]
 
 rule all:
     input:
         auspice_json = all_targets()
-        # sequences = expand("results/sequences_{subtype}_{segment}.fasta", subtype=SUBTYPES, segment=SEGMENTS),
-        # metadata = expand("results/metadata_{subtype}_{segment}.tsv", subtype=SUBTYPES, segment=SEGMENTS)
-
 
 rule files:
     params:
@@ -367,7 +364,7 @@ rule export:
         auspice_config = files.auspice_config,
         description = files.description
     output:
-        auspice_json = "auspice/flu_avian_{subtype}_{segment}_{time}.json"
+        auspice_json = "auspice/avian-flu_{subtype}_{segment}_{time}.json"
     shell:
         """
         augur export v2 \

diff --git a/batch.py b/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')

diff --git a/clade-labeling/h5n1-clades.tsv b/clade-labeling/h5n1-clades.tsv
@@ -17811,3 +17811,85 @@ A/caspiantern/Washington/23024996001original/2023	2.3.4.4b
 A/Chicken/Netherlands/24001946006010/2024	EA-nonGsGD
 A/Tuftedduck/Netherlands/1/2023	EA-nonGsGD
 A/chicken/Iraq/KVCL016/2015	?
+          A/Ph/ST/44/2004	2.3.2
+A/chicken/Vietnam/Raho77232263/2023	2.3.2.1e
+A/duck/Vietnam/Raho723S2874/2023	2.3.2.1e
+A/duck/Vietnam/Raho723S2490/2023	2.3.2.1e
+A/Vietnam/KhanhhoaRV1005/2024	2.3.2.1e
+A/duck/Vietnam/Raho723S2875/2023	2.3.2.1e
+A/muteswan/Poland/MB055L2/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A045/2024	2.3.4.4b
+A/Fox/Bayern/i193/2023	2.3.4.4b
+A/feline/USA/24008764001original/2024	2.3.4.4b
+A/henharrier/Parnu/TA2126003/2021	2.3.4.4b
+A/chicken/CzechRepublic/3529/2024	2.3.4.4b
+A/domesticduck/Poland/H69T2/2024	2.3.4.4b
+A/goose/Bayern/wv196/2023	2.3.4.4b
+A/feline/USA/24009116005original/2024	2.3.4.4b
+A/muteswan/Poland/MB085N/2024	2.3.4.4b
+A/feline/USA/24009311006original/2024	2.3.4.4b
+A/chicken/CzechRepublic/47202/2024	2.3.4.4b
+A/chicken/Poland/H79T2/2024	2.3.4.4b
+A/muteswan/Poland/MB055L1/2024	2.3.4.4b
+A/dairycattle/Texas/24008749002v/2024	2.3.4.4b
+A/feline/USA/24009116004original/2024	2.3.4.4b
+A/domesticduck/Poland/H52T1K2/2024	2.3.4.4b
+A/chicken/CzechRepublic/35494/2024	2.3.4.4b
+A/chicken/CzechRepublic/31374/2024	2.3.4.4b
+A/feline/USA/24009116002original/2024	2.3.4.4b
+A/chicken/CzechRepublic/3744orig/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A031/2024	2.3.4.4b
+A/muteswan/Poland/MB055L4/2024	2.3.4.4b
+A/domesticduck/Poland/H57T1/2024	2.3.4.4b
+A/turkey/Poland/H40T2/2024	2.3.4.4b
+A/goose/Bayern/wv351/2023	2.3.4.4b
+A/domesticgoose/Poland/H49W/2024	2.3.4.4b
+A/turkey/Poland/H47T4/2024	2.3.4.4b
+A/turkey/Poland/H80T3/2024	2.3.4.4b
+A/Texas/37/2024	2.3.4.4b
+A/chicken/Poland/H45NM/2024	2.3.4.4b
+A/turkey/Poland/H75T1/2024	2.3.4.4b
+A/CommonBuzzard/GermanyBB/2024AI01490/2024	2.3.4.4b
+A/feline/USA/23037332001original/2023	2.3.4.4b
+A/feline/USA/24008850001original/2024	2.3.4.4b
+A/turkey/Poland/H68T2/2024	2.3.4.4b
+A/domesticduck/Poland/H66T1/2024	2.3.4.4b
+A/feline/USA/24009311004original/2024	2.3.4.4b
+A/turkey/Poland/H43T2/2024	2.3.4.4b
+A/chicken/CzechRepublic/354910/2024	2.3.4.4b
+A/chicken/CzechRepublic/34582/2024	2.3.4.4b
+A/NorthernFulmar/Netherlands/4/2024	2.3.4.4b
+A/largebilledcrow/Ishikawa/1702A010/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A044/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A033/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A032/2024	2.3.4.4b
+A/chicken/CzechRepublic/37442/2024	2.3.4.4b
+A/domesticduck/Poland/H60T4/2024	2.3.4.4b
+A/feline/USA/24008850002original/2024	2.3.4.4b
+A/Seagull/Parnu/TA21132845/2021	2.3.4.4b
+A/chicken/CzechRepublic/37443/2024	2.3.4.4b
+A/muteswan/Poland/MB070L1/2024	2.3.4.4b
+A/buzzard/Poland/MB098N/2024	2.3.4.4b
+A/chicken/CzechRepublic/31371/2024	2.3.4.4b
+A/turkey/Poland/H81T1/2024	2.3.4.4b
+A/domesticgoose/Poland/H48D1/2024	2.3.4.4b
+A/chicken/CzechRepublic/37441/2024	2.3.4.4b
+A/muteswan/CzechRepublic/4316/2024	2.3.4.4b
+A/buzzard/Poland/MB103N/2024	2.3.4.4b
+A/turkey/Poland/H63N/2024	2.3.4.4b
+A/chicken/CzechRepublic/35499/2024	2.3.4.4b
+A/largebilledcrow/Hokkaido/B114/2024	2.3.4.4b
+A/chicken/CzechRepublic/34583/2024	2.3.4.4b
+A/feline/USA/24008764002original/2024	2.3.4.4b
+A/eagle/Parnu/TA21118641/2021	2.3.4.4b
+A/turkey/Poland/H38T4/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A043/2024	2.3.4.4b
+A/chicken/CzechRepublic/34584/2024	2.3.4.4b
+A/chicken/CzechRepublic/31375/2024	2.3.4.4b
+A/Northernshoveler/Jeju/D60/2023	2.3.4.4b
+A/turkey/Poland/H543NM/2023	2.3.4.4b
+A/largebilledcrow/Osaka/2702A030/2024	2.3.4.4b
+A/CommonBuzzard/GermanyHH/2024AI01435/2024	EA-nonGsGD
+A/BarnacleGoose/GermanySH/2024AI01487/2024	EA-nonGsGD
+A/Dunlin/GermanySH/2024AI01484/2024	EA-nonGsGD
+A/Fox/Bayern/WS113/2022	?
diff --git a/clade-labeling/h5nx-clades.tsv b/clade-labeling/h5nx-clades.tsv
@@ -26824,3 +26824,95 @@ A/Eurasianteal/Netherlands/2/2023	EA-nonGsGD
 A/Mallard/Netherlands/12/2023	EA-nonGsGD
 A/mallard/Poland/P292w10/2023	EA-nonGsGD
 A/chicken/Iraq/KVCL016/2015	?
+          A/Ph/ST/44/2004	2.3.2
+A/Vietnam/KhanhhoaRV1005/2024	2.3.2.1e
+A/duck/Vietnam/Raho723S2875/2023	2.3.2.1e
+A/chicken/Vietnam/Raho77232263/2023	2.3.2.1e
+A/duck/Vietnam/Raho723S2490/2023	2.3.2.1e
+A/duck/Vietnam/Raho723S2874/2023	2.3.2.1e
+A/largebilledcrow/Hokkaido/B114/2024	2.3.4.4b
+A/feline/USA/24008850002original/2024	2.3.4.4b
+A/chicken/CzechRepublic/47202/2024	2.3.4.4b
+A/chicken/CzechRepublic/34584/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A031/2024	2.3.4.4b
+A/henharrier/Parnu/TA2126003/2021	2.3.4.4b
+A/chicken/CzechRepublic/31375/2024	2.3.4.4b
+A/chicken/CzechRepublic/31371/2024	2.3.4.4b
+A/chicken/CzechRepublic/35499/2024	2.3.4.4b
+A/turkey/Poland/H75T1/2024	2.3.4.4b
+A/largebilledcrow/Hokkaido/B112/2024	2.3.4.4b
+A/chicken/Poland/H45NM/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A032/2024	2.3.4.4b
+A/buzzard/Poland/MB098N/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A033/2024	2.3.4.4b
+A/goose/Bayern/wv351/2023	2.3.4.4b
+A/feline/USA/24009116002original/2024	2.3.4.4b
+A/NorthernFulmar/Netherlands/3/2024	2.3.4.4b
+A/chicken/CzechRepublic/31374/2024	2.3.4.4b
+A/feline/USA/24008850001original/2024	2.3.4.4b
+A/feline/USA/24009311006original/2024	2.3.4.4b
+A/domesticduck/Poland/H60T4/2024	2.3.4.4b
+A/chicken/CzechRepublic/354910/2024	2.3.4.4b
+A/domesticgoose/Poland/H48D1/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A045/2024	2.3.4.4b
+A/domesticgoose/Poland/H49W/2024	2.3.4.4b
+A/turkey/Poland/H63N/2024	2.3.4.4b
+A/Texas/37/2024	2.3.4.4b
+A/buzzard/Poland/MB103N/2024	2.3.4.4b
+A/largebilledcrow/Ishikawa/1702A010/2024	2.3.4.4b
+A/NorthernFulmar/Netherlands/1/2024	2.3.4.4b
+A/domesticduck/Poland/H57T1/2024	2.3.4.4b
+A/chicken/CzechRepublic/37443/2024	2.3.4.4b
+A/turkey/Poland/H43T2/2024	2.3.4.4b
+A/CommonBuzzard/GermanyBB/2024AI01490/2024	2.3.4.4b
+A/Fox/Bayern/i193/2023	2.3.4.4b
+A/turkey/Poland/H38T4/2024	2.3.4.4b
+A/chicken/CzechRepublic/34583/2024	2.3.4.4b
+A/feline/USA/24009311004original/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A030/2024	2.3.4.4b
+A/NorthernFulmar/Netherlands/4/2024	2.3.4.4b
+A/chicken/CzechRepublic/34582/2024	2.3.4.4b
+A/Seagull/Parnu/TA21132845/2021	2.3.4.4b
+A/turkey/Poland/H68T2/2024	2.3.4.4b
+A/feline/USA/24009116004original/2024	2.3.4.4b
+A/muteswan/Poland/MB055L2/2024	2.3.4.4b
+A/largebilledcrow/Hokkaido/B104/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A044/2024	2.3.4.4b
+A/goose/Bayern/wv196/2023	2.3.4.4b
+A/feline/USA/24009116005original/2024	2.3.4.4b
+A/muteswan/CzechRepublic/4316/2024	2.3.4.4b
+A/turkey/Poland/H543NM/2023	2.3.4.4b
+A/chicken/CzechRepublic/37441/2024	2.3.4.4b
+A/muteswan/Poland/MB055L1/2024	2.3.4.4b
+A/Sparrowhawk/England/133485/2024	2.3.4.4b
+A/chicken/Poland/H79T2/2024	2.3.4.4b
+A/largebilledcrow/Osaka/2702A043/2024	2.3.4.4b
+A/muteswan/Poland/MB085N/2024	2.3.4.4b
+A/dairycattle/Texas/24008749002v/2024	2.3.4.4b
+A/feline/USA/23037332001original/2023	2.3.4.4b
+A/chicken/CzechRepublic/35494/2024	2.3.4.4b
+A/CommonBuzzard/England/133477/2024	2.3.4.4b
+A/chicken/CzechRepublic/3744orig/2024	2.3.4.4b
+A/feline/USA/24008764002original/2024	2.3.4.4b
+A/Northernshoveler/Jeju/D60/2023	2.3.4.4b
+A/Sparrowhawk/England/133522/2024	2.3.4.4b
+A/turkey/Poland/H81T1/2024	2.3.4.4b
+A/domesticduck/Poland/H52T1K2/2024	2.3.4.4b
+A/largebilledcrow/Hokkaido/B106/2024	2.3.4.4b
+A/chicken/CzechRepublic/3529/2024	2.3.4.4b
+A/eagle/Parnu/TA21118641/2021	2.3.4.4b
+A/muteswan/Poland/MB055L4/2024	2.3.4.4b
+A/feline/USA/24008764001original/2024	2.3.4.4b
+A/domesticduck/Poland/H69T2/2024	2.3.4.4b
+A/domesticduck/Poland/H66T1/2024	2.3.4.4b
+A/NorthernFulmar/Netherlands/2/2024	2.3.4.4b
+A/turkey/Poland/H47T4/2024	2.3.4.4b
+A/turkey/Poland/H80T3/2024	2.3.4.4b
+A/muteswan/Poland/MB070L1/2024	2.3.4.4b
+A/chicken/CzechRepublic/37442/2024	2.3.4.4b
+A/turkey/Poland/H40T2/2024	2.3.4.4b
+A/CommonBuzzard/GermanyHH/2024AI01435/2024	EA-nonGsGD
+A/RedKnot/GermanySH/2024AI01485/2024	EA-nonGsGD
+A/Dunlin/GermanySH/2024AI01484/2024	EA-nonGsGD
+A/BarnacleGoose/GermanySH/2024AI01487/2024	EA-nonGsGD
+A/Fox/Bayern/WS113/2022	?
diff --git a/config/include_strains_h5n1.txt b/config/include_strains_h5n1.txt
@@ -1,6 +1,7 @@
 A/Colorado/18/2022
 A/England/215201407/2021
 A/Astrakhan/3212/2020
+A/Goose/Guangdong/1/1996
 A/Mink/Spain/3691822VIR1058610/2022
 A/Mink/Spain/3691222VIR105868/2022
 A/Mink/Spain/36911022VIR1058611/2022

diff --git a/config/include_strains_h5nx.txt b/config/include_strains_h5nx.txt
@@ -1,6 +1,7 @@
 A/Colorado/18/2022
 A/England/215201407/2021
 A/Astrakhan/3212/2020
+A/Goose/Guangdong/1/1996
 A/Mink/Spain/3691822VIR1058610/2022
 A/Mink/Spain/3691222VIR105868/2022
 A/Mink/Spain/36911022VIR1058611/2022

diff --git a/quickstart-build/Snakefile b/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 \