diff --git a/Snakefile b/Snakefile index fa83424..986b38a 100755 --- a/Snakefile +++ b/Snakefile @@ -6,6 +6,7 @@ wildcard_constraints: # defined before extra rules `include`d as they reference this constant SEGMENTS = ["pb2", "pb1", "pa", "ha","np", "na", "mp", "ns"] +#SUBTYPES = ["h5n1", "h5nx", "h7n9", "h9n2"] # The config option `same_strains_per_segment=True'` (e.g. supplied to snakemake via --config command line argument) # will change the behaviour of the workflow to use the same strains for each segment. This is achieved via these steps: @@ -46,6 +47,9 @@ def collect_builds(): rule all: input: auspice_json = collect_builds() + #sequences = expand("results/{subtype}/{segment}/sequences.fasta", segment=SEGMENTS, subtype=SUBTYPES), + #metadata = expand("results/{subtype}/metadata.tsv", segment=SEGMENTS, subtype=SUBTYPES) + # This must be after the `all` rule above since it depends on its inputs include: "rules/deploy.smk" diff --git a/clade-labeling/h5n1-clades.tsv b/clade-labeling/h5n1-clades.tsv index c634168..02d1532 100755 --- a/clade-labeling/h5n1-clades.tsv +++ b/clade-labeling/h5n1-clades.tsv @@ -22834,3 +22834,224 @@ A/Chicken/BC/FAV-0268-1/2024 2.3.4.4b A/British_Columbia/PHL-2032/2024 2.3.4.4b A/Turkey/BC/FAV-0267-1/2024 2.3.4.4b A/Chicken/BC/FAV-0285-1/2024 2.3.4.4b +A/chicken/USA/24031666025/2024 2.3.4.4b +A/BritishColumbia/PHL2032/2024 2.3.4.4b +A/turkey/USA/24031284027/2024 2.3.4.4b +A/chicken/USA/24031862008/2024 2.3.4.4b +A/chicken/USA/24031666013/2024 2.3.4.4b +A/chicken/USA/24031666029/2024 2.3.4.4b +A/dairycow/USA/24032027002/2024 2.3.4.4b +A/chicken/USA/24031862006/2024 2.3.4.4b +A/dairycow/USA/24032040001/2024 2.3.4.4b +A/chicken/USA/24031862018/2024 2.3.4.4b +A/chicken/USA/24031285014/2024 2.3.4.4b +A/dairycow/USA/24032022005/2024 2.3.4.4b +A/chicken/USA/24031286006/2024 2.3.4.4b +A/turkey/USA/24031284017/2024 2.3.4.4b +A/dairycow/USA/24032026003/2024 2.3.4.4b +A/dairycow/USA/24032016003/2024 2.3.4.4b +A/turkey/USA/24031284025/2024 2.3.4.4b +A/dairycow/USA/24031619009/2024 2.3.4.4b +A/chicken/USA/24031285004/2024 2.3.4.4b +A/turkey/USA/24031284028/2024 2.3.4.4b +A/turkey/USA/24031284018/2024 2.3.4.4b +A/greygoose/Austria/24144112/2024 2.3.4.4b +A/emu/USA/24031663004/2024 2.3.4.4b +A/dairycow/USA/24032049003/2024 2.3.4.4b +A/dairycow/USA/24032042001/2024 2.3.4.4b +A/dairycow/USA/24032027004/2024 2.3.4.4b +A/chicken/USA/24031862017/2024 2.3.4.4b +A/dairycow/USA/24032023004/2024 2.3.4.4b +A/turkey/USA/24031284029/2024 2.3.4.4b 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2.3.4.4b +A/turkey/USA/24031284023/2024 2.3.4.4b +A/dairycow/USA/24032045001/2024 2.3.4.4b +A/chicken/USA/24031285009/2024 2.3.4.4b +A/chicken/USA/24031285005/2024 2.3.4.4b +A/chicken/USA/24031666018/2024 2.3.4.4b +A/dairycow/USA/24032035002/2024 2.3.4.4b +A/chicken/USA/24031666022/2024 2.3.4.4b +A/turkey/USA/24031284020/2024 2.3.4.4b +A/dairycow/USA/24032049001/2024 2.3.4.4b +A/dairycow/USA/24032049002/2024 2.3.4.4b +A/dairycow/USA/24032057002/2024 2.3.4.4b +A/chicken/USA/24031285006/2024 2.3.4.4b +A/chicken/USA/24031667005/2024 2.3.4.4b +A/dairycow/USA/24032027001/2024 2.3.4.4b +A/dairycow/USA/24032027005/2024 2.3.4.4b +A/chicken/USA/24031666015/2024 2.3.4.4b +A/chicken/USA/24031666028/2024 2.3.4.4b +A/chicken/USA/24031666017/2024 2.3.4.4b +A/dairycow/USA/24031627002/2024 2.3.4.4b +A/turkey/USA/24031284006/2024 2.3.4.4b +A/dairycow/USA/24032035004/2024 2.3.4.4b +A/dairycow/USA/24031627005/2024 2.3.4.4b +A/dairycow/USA/24031340001/2024 2.3.4.4b +A/dairycow/USA/24032016002/2024 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2.3.4.4b +A/muteswan/Austria/24144823001/2024 2.3.4.4b +A/chicken/USA/24031666005/2024 2.3.4.4b +A/chicken/USA/24031666024/2024 2.3.4.4b +A/dairycow/USA/24032021001/2024 2.3.4.4b +A/dairycow/USA/24031340004/2024 2.3.4.4b +A/chicken/USA/24031285012/2024 2.3.4.4b +A/dairycow/USA/24032036001/2024 2.3.4.4b +A/chicken/USA/24031286003/2024 2.3.4.4b +A/Chicken/BritishColumbia/FAV02661/2024 2.3.4.4b +A/muteswan/Austria/24145572/2024 2.3.4.4b +A/dairycow/USA/24032022001/2024 2.3.4.4b +A/dairycow/USA/24031489002/2024 2.3.4.4b +A/chicken/USA/24031285015/2024 2.3.4.4b +A/chicken/USA/24031666019/2024 2.3.4.4b +A/chicken/USA/24031285002/2024 2.3.4.4b +A/dairycow/USA/24032035003/2024 2.3.4.4b +A/dairycow/USA/24032206001/2024 2.3.4.4b +A/dairycow/USA/24031626004/2024 2.3.4.4b +A/dairycow/USA/24032021002/2024 2.3.4.4b +A/dairycow/USA/24031494001/2024 2.3.4.4b +A/dairycow/USA/24032046002/2024 2.3.4.4b +A/chicken/USA/24031285003/2024 2.3.4.4b +A/turkey/USA/24031284004/2024 2.3.4.4b 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2.3.4.4b +A/dairycow/USA/24031317004/2024 ? diff --git a/clade-labeling/h5nx-clades.tsv b/clade-labeling/h5nx-clades.tsv index fca21db..2d00b41 100755 --- a/clade-labeling/h5nx-clades.tsv +++ b/clade-labeling/h5nx-clades.tsv @@ -32071,3 +32071,225 @@ A/Chicken/BC/FAV-0266-1/2024 2.3.4.4b A/British_Columbia/PHL-2032/2024 2.3.4.4b A/Chicken/BC/FAV-0268-1/2024 2.3.4.4b A/Turkey/BC/FAV-0267-1/2024 2.3.4.4b +A/chicken/USA/24031862018/2024 2.3.4.4b +A/dairycow/USA/24032021001/2024 2.3.4.4b +A/chicken/USA/24031666014/2024 2.3.4.4b +A/dairycow/USA/24032022001/2024 2.3.4.4b +A/chicken/USA/24031666020/2024 2.3.4.4b +A/dairycow/USA/24032199001/2024 2.3.4.4b +A/chicken/USA/24031285009/2024 2.3.4.4b +A/turkey/USA/24031284022/2024 2.3.4.4b +A/dairycow/USA/24032016001/2024 2.3.4.4b +A/turkey/USA/24031284017/2024 2.3.4.4b +A/dairycow/USA/24031627002/2024 2.3.4.4b +A/dairycow/USA/24031619002/2024 2.3.4.4b +A/dairycow/USA/24032045001/2024 2.3.4.4b +A/chicken/USA/24031666011/2024 2.3.4.4b 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+++ b/config/h5n1-cattle-outbreak/dropped_strains_h5n1-cattle-outbreak.txt @@ -197,6 +197,8 @@ A/Turkey/USA/24-007379-002-original/2024 A/turkeyvulture/California/24-007419-001/2024 A/TurkeyVulture/USA/24-007419-001-original/2024 A/Washington/240/2024 +A/Washington/239/2024 +A/Washington/255/2024 A/Washington/UW32495/2024 A/westerngull/California/24-004708-001/2024 A/WesternGull/USA/24-004708-001-original/2024