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private.nextflu.org.yaml
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private.nextflu.org.yaml
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custom_rules:
- workflow/snakemake_rules/download_from_s3.smk
- profiles/private.nextflu.org/export.smk
lat-longs: "config/lat_longs.tsv"
segments:
- ha
tree:
tree-builder-args: "'-ninit 10 -n 4 -czb'"
submission_date_field: date_submitted
recency:
date_bins: [7, 30, 90]
date_bin_labels: ["last week", "last month", "last quarter"]
upper_bin_label: older
array-builds:
2Y-hi-builds:
patterns:
center:
- who
- cdc
- crick
- niid
- vidrl
lineage:
- h3n2
- h1n1pdm
- vic
passage:
- cell
- egg
assay:
- hi
min_date:
- 2Y
reference_min_date:
- 8Y
resolution:
- 2y
build_name: "flu_{center}_{lineage}_{resolution}_{passage}_{assay}"
build_params: &shared-build-params
auspice_name: "flu_{center}_{lineage}_{{segment}}_{resolution}_{passage}_{assay}"
reference: "config/{lineage}/{{segment}}/reference.fasta"
annotation: "config/{lineage}/{{segment}}/genemap.gff"
tree_exclude_sites: "config/{lineage}/{{segment}}/exclude-sites.txt"
clades: "config/{lineage}/ha/clades.tsv"
auspice_config: "config/{lineage}/auspice_config_who.json"
vaccines: "config/{lineage}/vaccine.json"
enable_glycosylation: true
enable_lbi: true
enable_titer_models: true
include: "config/{lineage}/reference_strains.txt"
exclude: "config/{lineage}/outliers.txt"
titer_collections:
- name: titers
data: "data/{lineage}/{center}_ferret_{passage}_{assay}_titers.tsv"
subsamples: &subsampling-scheme
regions_except_europe:
filters: --query "(passage_category in ['{passage}', 'cell', 'unpassaged', 'undetermined', 'N/A']) & (region != 'Europe')" --group-by region year month --subsample-max-sequences 2700 --min-date {min_date} --exclude {exclude} --exclude-where country=? region=?
priorities: "titers"
europe:
filters: --query "(passage_category in ['{passage}', 'cell', 'unpassaged', 'undetermined', 'N/A']) & (region == 'Europe')" --group-by country year month --subsample-max-sequences 300 --min-date {min_date} --exclude {exclude} --exclude-where country=? region=?
priorities: "titers"
references:
filters: --query "(is_reference == True)" --min-date {reference_min_date}
6Y-hi-builds:
patterns:
center:
- who
- cdc
- crick
- niid
- vidrl
lineage:
- h3n2
- h1n1pdm
- vic
passage:
- cell
- egg
assay:
- hi
min_date:
- 6Y
reference_min_date:
- 12Y
resolution:
- 6y
build_name: "flu_{center}_{lineage}_{resolution}_{passage}_{assay}"
build_params: *shared-build-params
subsamples: *subsampling-scheme
2Y-fra-builds:
patterns:
center:
- who
- cdc
- crick
- niid
- vidrl
lineage:
- h3n2
passage:
- cell
- egg
assay:
- fra
min_date:
- 2Y
reference_min_date:
- 8Y
resolution:
- 2y
build_name: "flu_{center}_{lineage}_{resolution}_{passage}_{assay}"
build_params: *shared-build-params
subsamples: *subsampling-scheme
6Y-fra-builds:
patterns:
center:
- who
- cdc
- crick
- niid
- vidrl
lineage:
- h3n2
passage:
- cell
- egg
assay:
- fra
min_date:
- 6Y
reference_min_date:
- 12Y
resolution:
- 6y
build_name: "flu_{center}_{lineage}_{resolution}_{passage}_{assay}"
build_params: *shared-build-params
subsamples: *subsampling-scheme