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upload.yaml
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upload.yaml
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custom_rules:
- profiles/upload/upload.smk
s3_dst: "s3://nextstrain-data-private/files/workflows/seasonal-flu"
data_source: fauna
fauna_fasta_fields:
- strain
- virus
- locus
- isolate_id
- accession
- collection_date
- submission_date
- region
- country
- division
- location
- passage_category
- originating_lab
- submitting_lab
- age
- gender
fasta_fields:
- strain
- virus
- segment
- isolate_id
- accession
- date
- date_submitted
- region
- country
- division
- location
- passage_category
- originating_lab
- submitting_lab
- age
- gender
prettify_fields:
- region
- country
- division
- location
- originating_lab
- submitting_lab
lat-longs: "config/lat_longs.tsv"
segments:
- ha
- na
tree:
method: iqtree
tree-builder-args: "'-ninit 10 -n 4 -czb -nt AUTO'"
override_default_args: true
submission_date_field: date_submitted
recency:
date_bins: [7, 30, 90]
date_bin_labels: ["last week", "last month", "last quarter"]
upper_bin_label: older
builds:
h1n1pdm_2y:
lineage: h1n1pdm
reference: "config/h1n1pdm/{segment}/reference.fasta"
annotation: "config/h1n1pdm/{segment}/genemap.gff"
tree_exclude_sites: "config/h1n1pdm/{segment}/exclude-sites.txt"
clades: "config/h1n1pdm/ha/clades.tsv"
auspice_config: "config/h1n1pdm/auspice_config.json"
min_date: "2Y"
reference_min_date: "8Y"
include: "config/h1n1pdm/reference_strains.txt"
exclude: "config/h1n1pdm/outliers.txt"
vaccines: "config/h1n1pdm/vaccine.json"
titer_collections:
- name: who_ferret_cell_hi
data: "data/h1n1pdm/who_ferret_cell_hi_titers.tsv"
- name: who_ferret_egg_hi
data: "data/h1n1pdm/who_ferret_egg_hi_titers.tsv"
- name: who_human_cell_hi
data: "data/h1n1pdm/who_human_cell_hi_titers.tsv"
- name: who_mouse_cell_hi
data: "data/h1n1pdm/who_mouse_cell_hi_titers.tsv"
- name: cdc_ferret_cell_hi
data: "data/h1n1pdm/cdc_ferret_cell_hi_titers.tsv"
- name: cdc_ferret_egg_hi
data: "data/h1n1pdm/cdc_ferret_egg_hi_titers.tsv"
- name: crick_ferret_cell_hi
data: "data/h1n1pdm/crick_ferret_cell_hi_titers.tsv"
- name: crick_ferret_egg_hi
data: "data/h1n1pdm/crick_ferret_egg_hi_titers.tsv"
- name: niid_ferret_cell_hi
data: "data/h1n1pdm/niid_ferret_cell_hi_titers.tsv"
- name: niid_ferret_egg_hi
data: "data/h1n1pdm/niid_ferret_egg_hi_titers.tsv"
- name: vidrl_ferret_cell_hi
data: "data/h1n1pdm/vidrl_ferret_cell_hi_titers.tsv"
- name: vidrl_ferret_egg_hi
data: "data/h1n1pdm/vidrl_ferret_egg_hi_titers.tsv"
subsamples: &representative-subsampling-scheme
regions_except_europe:
filters: --query "(passage_category != 'egg') & (region != 'Europe') & (ha == True) & (na == True)" --group-by region year month --subsample-max-sequences 1800 --min-date {min_date} --exclude {exclude}
priorities: "titers"
europe:
filters: --query "(passage_category != 'egg') & (region == 'Europe') & (ha == True) & (na == True)" --group-by country year month --subsample-max-sequences 200 --min-date {min_date} --exclude {exclude}
priorities: "titers"
context:
filters: --query "(passage_category != 'egg')" --group-by region year --subsample-max-sequences 300 --max-date 2020-03-01 --min-date 2016-01-01 --exclude {exclude}
references:
filters: --query "(passage_category != 'egg') & (is_reference == True)" --min-date {reference_min_date}
h3n2_2y:
lineage: "h3n2"
reference: "config/h3n2/{segment}/reference.fasta"
annotation: "config/h3n2/{segment}/genemap.gff"
tree_exclude_sites: "config/h3n2/{segment}/exclude-sites.txt"
clades: "config/h3n2/ha/emerging_clades.tsv"
auspice_config: "config/h3n2/auspice_config_fitness.json"
vaccines: "config/h3n2/vaccine.json"
min_date: "2Y"
reference_min_date: "8Y"
include: "config/h3n2/reference_strains.txt"
exclude: "config/h3n2/outliers.txt"
titer_collections:
- name: who_ferret_cell_fra
data: "data/h3n2/who_ferret_cell_fra_titers.tsv"
- name: who_ferret_egg_fra
data: "data/h3n2/who_ferret_egg_fra_titers.tsv"
- name: who_ferret_cell_hi
data: "data/h3n2/who_ferret_cell_hi_titers.tsv"
- name: who_ferret_egg_hi
data: "data/h3n2/who_ferret_egg_hi_titers.tsv"
- name: who_human_cell_fra
data: "data/h3n2/who_human_cell_fra_titers.tsv"
- name: who_human_cell_hi
data: "data/h3n2/who_human_cell_hi_titers.tsv"
- name: cdc_ferret_cell_hi
data: "data/h3n2/cdc_ferret_cell_hi_titers.tsv"
- name: cdc_ferret_egg_hi
data: "data/h3n2/cdc_ferret_egg_hi_titers.tsv"
- name: crick_ferret_cell_hi
data: "data/h3n2/crick_ferret_cell_hi_titers.tsv"
- name: crick_ferret_egg_hi
data: "data/h3n2/crick_ferret_egg_hi_titers.tsv"
- name: niid_ferret_cell_hi
data: "data/h3n2/niid_ferret_cell_hi_titers.tsv"
- name: niid_ferret_egg_hi
data: "data/h3n2/niid_ferret_egg_hi_titers.tsv"
- name: vidrl_ferret_cell_hi
data: "data/h3n2/vidrl_ferret_cell_hi_titers.tsv"
- name: vidrl_ferret_egg_hi
data: "data/h3n2/vidrl_ferret_egg_hi_titers.tsv"
- name: cdc_ferret_cell_fra
data: "data/h3n2/cdc_ferret_cell_fra_titers.tsv"
- name: cdc_ferret_egg_fra
data: "data/h3n2/cdc_ferret_egg_fra_titers.tsv"
- name: crick_ferret_cell_fra
data: "data/h3n2/crick_ferret_cell_fra_titers.tsv"
- name: crick_ferret_egg_fra
data: "data/h3n2/crick_ferret_egg_fra_titers.tsv"
- name: niid_ferret_cell_fra
data: "data/h3n2/niid_ferret_cell_fra_titers.tsv"
- name: niid_ferret_egg_fra
data: "data/h3n2/niid_ferret_egg_fra_titers.tsv"
- name: vidrl_ferret_cell_fra
data: "data/h3n2/vidrl_ferret_cell_fra_titers.tsv"
- name: vidrl_ferret_egg_fra
data: "data/h3n2/vidrl_ferret_egg_fra_titers.tsv"
subsamples: *representative-subsampling-scheme
vic_2y:
lineage: vic
reference: "config/vic/{segment}/reference.fasta"
annotation: "config/vic/{segment}/genemap.gff"
tree_exclude_sites: "config/vic/{segment}/exclude-sites.txt"
clades: "config/vic/ha/clades.tsv"
auspice_config: "config/vic/auspice_config.json"
min_date: "2Y"
reference_min_date: "8Y"
include: "config/vic/reference_strains.txt"
exclude: "config/vic/outliers.txt"
vaccines: "config/vic/vaccine.json"
titer_collections:
- name: who_ferret_cell_hi
data: "data/vic/who_ferret_cell_hi_titers.tsv"
- name: who_ferret_egg_hi
data: "data/vic/who_ferret_egg_hi_titers.tsv"
- name: who_human_cell_hi
data: "data/vic/who_human_cell_hi_titers.tsv"
- name: cdc_ferret_cell_hi
data: "data/vic/cdc_ferret_cell_hi_titers.tsv"
- name: cdc_ferret_egg_hi
data: "data/vic/cdc_ferret_egg_hi_titers.tsv"
- name: crick_ferret_cell_hi
data: "data/vic/crick_ferret_cell_hi_titers.tsv"
- name: crick_ferret_egg_hi
data: "data/vic/crick_ferret_egg_hi_titers.tsv"
- name: niid_ferret_cell_hi
data: "data/vic/niid_ferret_cell_hi_titers.tsv"
- name: niid_ferret_egg_hi
data: "data/vic/niid_ferret_egg_hi_titers.tsv"
- name: vidrl_ferret_cell_hi
data: "data/vic/vidrl_ferret_cell_hi_titers.tsv"
- 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