Merge pull request #124 from nextstrain/nextclade

Nextclade

Snakefile

@@ -4,7 +4,7 @@ from treetime.utils import numeric_date
 
 
 wildcard_constraints:
-    segment = r'pb2|pb1|pa|ha|np|na|ma',
+    segment = r'pb2|pb1|pa|ha|np|na|mp|ns',
     center = r'who|cdc|crick|niid|crick|vidrl',
     passage = r'cell|egg',
     assay = r'fra|hi',

config/h1n1pdm/outliers.txt

@@ -10,6 +10,7 @@ A/Asturias/RR6898/2010
 A/Austria/1048413/2018
 A/Austria/183/2009-egg
 A/Bangladesh/2021/2012
+A/Bangkok/P1600/2023
 A/Bari/166/2016
 A/Bari/167/2016
 A/Beijing/1/2009-egg
@@ -51,6 +52,7 @@ A/India/4562/2021
 A/India/8484/2021
 A/India/9324/2021
 A/India/9825/2021
+A/India/CT-AIIMSR-266/2022
 A/India/Pun1418633/2014
 A/India/TS-NIV2019nCoV177/2020
 A/Iowa/1/2006
@@ -67,6 +69,7 @@ A/Louisiana/EVTL-100047/2022
 A/Malaysia/2142295/2009
 A/Malaysia/2142299/2009
 A/Malaysia/2143696/2009
+A/Manitoba/2/2021
 A/Minnesota/3/2008
 A/Minnesota/33/2014
 A/Minnesota/46/2015
@@ -110,6 +113,7 @@ A/Rennes/F_006_111_BL/2020
 A/Rennes/F_006_119_JD/2020
 A/RheinlandPfalz/1/2020
 A/RioGrandedoNorte/117490/2012
+A/RioGrandeDoNorte/2023-012263-IEC/2023
 A/SaintLucia/7340/2020
 A/Shandong/1/2009
 A/Shandong/1/2009-egg
@@ -123,6 +127,7 @@ A/SouthAfrica/16112/2021
 A/SouthAfrica/16325/2021
 A/SouthAfrica/1857/2013
 A/SouthAfrica/NHLS-UCT-GS-0017/2021
+A/SouthAfrica/NHLS-UCT-GS-0034/2021
 A/SouthAfrica/PET20279/2021
 A/SouthDakota/3/2008
 A/SriLanka/11/2012

config/h1n1pdm/reference_strains.txt

@@ -5,7 +5,6 @@ A/Arizona/33/2017
 A/Arkansas/4/2020
 A/Arkansas/8/2020
 A/Arkansas/8/2020-egg
-A/Austria/1048413/2018
 A/Bangladesh/2021/2012
 A/Bangladesh/3002/2015
 A/Bolivia/559/2013

config/h3n2/outliers.txt

@@ -10,6 +10,9 @@ A/Austria/839906/2015
 A/Bangladesh/3010/2020
 A/BosniaandHerzegovia/288G/2019
 A/Brazil/BA-LACEN-BA053-292045410/2022
+A/Brazil/BA-LACEN-BA071-292012660/2021
+A/Brazil/BA-LACEN-BA123-292029844/2021
+A/Brazil/BA-LACEN-BA128-292008241/2021
 A/Busan/15453/2009
 A/California/NHRC0001/2011
 A/Cambodia/NHRCC00001/2009
@@ -27,6 +30,8 @@ A/Catalonia/NSVH100570896/2017
 A/Catalonia/NSVH100731127/2017
 A/Catalonia/NSVH100748648/2018
 A/Catalonia/NSVH100751838/2018
+A/ChiangRai/NIC-P3252/2022
+A/ChiangRai/D1249/2022
 A/Chile/8266/2003
 A/Corsica/10/2009
 A/Corsica/11/2008
@@ -45,6 +50,7 @@ A/Corsica/39/2009
 A/Corsica/42/2009
 A/Corsica/7/2007
 A/Cyprus/F83/2017
+A/Dakar/922/2022
 A/Darwin/143/2020
 A/Delaware/3/2011
 A/Delaware/33/2017
@@ -463,6 +469,7 @@ A/Sedbury/2991/2023
 A/Shanghai-Minxing/1482/2017
 A/Shanghai/6/2014
 A/Singapore/GP11121/2022
+A/SouthAfrica/K056301/2023
 A/SouthAustralia/1/2021
 A/SouthAustralia/22/2018
 A/SouthAustralia/47/2016

config/vic/outliers.txt

@@ -3,6 +3,7 @@ B/Alagoas/4386/2023
 B/Auckland/1/2008
 B/Bangkok/SI17/2012
 B/Bangkok/SI58/2012
+B/Bari/53/2023
 B/Brisbane/14/2016
 B/Brisbine/33/2008
 B/California/87/2017-egg

config/yam/outliers.txt

@@ -9,6 +9,7 @@ B/Kolkata/N-2047/2009
 B/Nairobi/351/2005
 B/NewHampshire/1/2016
 B/Norway/2155/2017
+B/Palermo/2/2011
 B/Riyadh/3/2010
 B/Riyadh/4/2010
 B/Thailand/CU-B10303/2014