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adding Washington strain to exclude list and updating clade assignments
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@lmoncla
lmoncla committed Nov 20, 2024
1 parent da8a4f9 commit 1895865
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4 changes: 4 additions & 0 deletions Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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"
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221 changes: 221 additions & 0 deletions clade-labeling/h5n1-clades.tsv
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Expand Up @@ -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
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A/chicken/USA/24031862018/2024 2.3.4.4b
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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
A/dairycow/USA/24032024002/2024 2.3.4.4b
A/turkey/USA/24031284014/2024 2.3.4.4b
A/chicken/USA/24031285008/2024 2.3.4.4b
A/muteswan/Austria/24143648/2024 2.3.4.4b
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A/dairycow/USA/24032026002/2024 2.3.4.4b
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A/dairycow/USA/24032025001/2024 2.3.4.4b
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A/dairycow/USA/24031627001/2024 2.3.4.4b
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A/dairycow/USA/24032013001/2024 2.3.4.4b
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A/dairycow/USA/24032022008/2024 2.3.4.4b
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A/dairycow/USA/24032019001/2024 2.3.4.4b
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A/dairycow/USA/24031627002/2024 2.3.4.4b
A/turkey/USA/24031284006/2024 2.3.4.4b
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A/dairycow/USA/24031627005/2024 2.3.4.4b
A/dairycow/USA/24031340001/2024 2.3.4.4b
A/dairycow/USA/24032016002/2024 2.3.4.4b
A/dairycow/USA/24032056002/2024 2.3.4.4b
A/dairycow/USA/24032028001/2024 2.3.4.4b
A/turkey/USA/24031284026/2024 2.3.4.4b
A/chicken/USA/24031286001/2024 2.3.4.4b
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A/turkey/USA/24031284021/2024 2.3.4.4b
A/chicken/USA/24031667006/2024 2.3.4.4b
A/muteswan/Austria/24144670/2024 2.3.4.4b
A/chicken/USA/24031286011/2024 2.3.4.4b
A/dairycow/USA/24032054004/2024 2.3.4.4b
A/dairycow/USA/24032013003/2024 2.3.4.4b
A/greygoose/Austria/24145594/2024 2.3.4.4b
A/chicken/USA/24031285010/2024 2.3.4.4b
A/turkey/USA/24031284010/2024 2.3.4.4b
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A/dairycow/USA/24032034001/2024 2.3.4.4b
A/muteswan/Austria/24142228001/2024 2.3.4.4b
A/dairycow/USA/24032016001/2024 2.3.4.4b
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A/chicken/USA/24031862013/2024 2.3.4.4b
A/muteswan/Austria/24144842001/2024 2.3.4.4b
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A/chicken/USA/24031666027/2024 2.3.4.4b
A/chicken/USA/24031862016/2024 2.3.4.4b
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A/dairycow/USA/24032021004/2024 2.3.4.4b
A/turkey/USA/24031284001/2024 2.3.4.4b
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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
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A/turkey/USA/24031284009/2024 2.3.4.4b
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A/dairycow/USA/24031959001/2024 2.3.4.4b
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A/chicken/USA/24031862009/2024 2.3.4.4b
A/dairycow/USA/24031957001/2024 2.3.4.4b
A/turkey/USA/24031284008/2024 2.3.4.4b
A/dairycow/USA/24032013002/2024 2.3.4.4b
A/dairycow/USA/24031619002/2024 2.3.4.4b
A/dairycow/USA/24031619007/2024 2.3.4.4b
A/chicken/USA/24031286010/2024 2.3.4.4b
A/chicken/USA/24031666014/2024 2.3.4.4b
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A/dairycow/USA/24031622002/2024 2.3.4.4b
A/turkey/USA/24031284003/2024 2.3.4.4b
A/Turkey/BritishColumbia/FAV02671/2024 2.3.4.4b
A/dairycow/USA/24032007002/2024 2.3.4.4b
A/dairycow/USA/24032026004/2024 2.3.4.4b
A/chicken/USA/24031666011/2024 2.3.4.4b
A/dairycow/USA/24032030001/2024 2.3.4.4b
A/dairycow/USA/24031317004/2024 ?
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