diff --git a/config/h1n1pdm/ha/auspice_config.json b/config/h1n1pdm/ha/auspice_config.json new file mode 100644 index 00000000..40239891 --- /dev/null +++ b/config/h1n1pdm/ha/auspice_config.json @@ -0,0 +1,243 @@ +{ + "title": "Real-time tracking of influenza A/H1N1pdm evolution", + "maintainers": [ + { + "name": "Jennifer Chang", + "url": "https://bedford.io/team/jennifer-chang/" + }, + { + "name": "Jover Lee", + "url": "https://bedford.io/team/jover-lee/" + }, + { + "name": "John Huddleston", + "url": "https://bedford.io/team/john-huddleston/" + }, + { + "name": "Richard Neher", + "url": "https://neherlab.org/richard-neher.html" + }, + { + "name": "Trevor Bedford", + "url": "https://bedford.io/team/trevor-bedford/" + } + ], + "data_provenance": [ + { + "name": "GISAID" + } + ], + "build_url": "https://github.com/nextstrain/seasonal-flu", + "colorings": [ + { + "key": "gt", + "title": "Genotype", + "type": "categorical" + }, + { + "key": "num_date", + "title": "Date", + "type": "continuous" + }, + { + "key": "clade_membership", + "title": "Clade", + "type": "categorical" + }, + { + "key": "subclade", + "title": "Subclade", + "type": "categorical", + "scale": [ + [ + "C.1", + "#492AB5" + ], + [ + "C.1.1", + "#3F4CCB" + ], + [ + "C.1.2", + "#4271CE" + ], + [ + "C.1.5", + "#4C8FC0" + ], + [ + "C.1.7", + "#5AA5A8" + ], + [ + "C.1.7.1", + "#6DB38A" + ], + [ + "C.1.7.2", + "#85BA6F" + ], + [ + "C.1.8", + "#A0BE59" + ], + [ + "C.1.9", + "#BBBC49" + ], + [ + "D", + "#D2B340" + ], + [ + "D.1", + "#E19F3A" + ], + [ + "D.2", + "#E68033" + ], + [ + "D.3", + "#E2562B" + ], + [ + "D.4", + "#DB2823" + ] + ] + }, + { + "key": "haplotype", + "title": "Derived haplotype", + "type": "categorical" + }, + { + "key": "cTiter", + "title": "Antigenic advance (tree model)", + "type": "continuous" + }, + { + "key": "cTiterSub", + "title": "Antigenic advance (sub model)", + "type": "continuous" + }, + { + "key": "cTiter_x", + "title": "HI antigenic novelty", + "type": "continuous" + }, + { + "key": "lbi", + "title": "Local branching index", + "type": "continuous" + }, + { + "key": "ep", + "title": "Epitope mutations", + "type": "continuous" + }, + { + "key": "ne", + "title": "Non-epitope mutations", + "type": "continuous" + }, + { + "key": "glyc", + "title": "Glycosylation changes", + "type": "continuous" + }, + { + "key": "region", + "title": "Region", + "type": "categorical" + }, + { + "key": "country", + "title": "Country", + "type": "categorical" + }, + { + "key": "division", + "title": "Division", + "type": "categorical" + }, + { + "key": "accession_ha", + "title": "Accession (HA)", + "type": "categorical" + }, + { + "key": "accession_na", + "title": "Accession (NA)", + "type": "categorical" + }, + { + "key": "submitting_lab", + "title": "Submitting lab", + "type": "categorical" + }, + { + "key": "originating_lab", + "title": "Originating lab", + "type": "categorical" + }, + { + "key": "recency", + "title": "Submission date", + "type": "ordinal" + }, + { + "key": "epiweek", + "title": "Epiweek (CDC)", + "type": "ordinal" + }, + { + "key": "year_month", + "title": "Year/month", + "type": "categorical" + }, + { + "key": "tsne_x", + "title": "t-SNE 1", + "type": "continuous" + }, + { + "key": "tsne_y", + "title": "t-SNE 2", + "type": "continuous" + }, + { + "key": "tsne_cluster", + "title": "t-SNE cluster", + "type": "categorical" + } + ], + "geo_resolutions": [ + "division", + "country", + "region" + ], + "display_defaults": { + "map_triplicate": true, + "color_by": "clade_membership" + }, + "filters": [ + "clade_membership", + "subclade", + "region", + "country", + "division", + "submitting_lab", + "recency", + "epiweek", + "year_month", + "tsne_cluster" + ], + "panels": [ + "tree", + "map", + "entropy", + "frequencies" + ] +} diff --git a/config/h1n1pdm/na/auspice_config.json b/config/h1n1pdm/na/auspice_config.json new file mode 100644 index 00000000..f3417541 --- /dev/null +++ b/config/h1n1pdm/na/auspice_config.json @@ -0,0 +1,208 @@ +{ + "title": "Real-time tracking of influenza A/H1N1pdm evolution", + "maintainers": [ + { + "name": "Jennifer Chang", + "url": "https://bedford.io/team/jennifer-chang/" + }, + { + "name": "Jover Lee", + "url": "https://bedford.io/team/jover-lee/" + }, + { + "name": "John Huddleston", + "url": "https://bedford.io/team/john-huddleston/" + }, + { + "name": "Richard Neher", + "url": "https://neherlab.org/richard-neher.html" + }, + { + "name": "Trevor Bedford", + "url": "https://bedford.io/team/trevor-bedford/" + } + ], + "data_provenance": [ + { + "name": "GISAID" + } + ], + "build_url": "https://github.com/nextstrain/seasonal-flu", + "colorings": [ + { + "key": "gt", + "title": "Genotype", + "type": "categorical" + }, + { + "key": "num_date", + "title": "Date", + "type": "continuous" + }, + { + "key": "clade_membership", + "title": "Clade", + "type": "categorical" + }, + { + "key": "subclade", + "title": "Subclade", + "type": "categorical", + "scale": [ + [ + "C", + "#3E5DD0" + ], + [ + "C.3", + "#4A8CC2" + ], + [ + "C.4", + "#60AA9E" + ], + [ + "C.5.1.1", + "#80B974" + ], + [ + "C.5.2", + "#A6BE55" + ], + [ + "C.5.3", + "#CBB742" + ], + [ + "C.5.3.1", + "#E29D39" + ], + [ + "C.5.3.2", + "#E56A2F" + ], + [ + "C.5.3.3", + "#DB2823" + ] + ] + }, + { + "key": "haplotype", + "title": "Derived haplotype", + "type": "categorical" + }, + { + "key": "lbi", + "title": "Local branching index", + "type": "continuous" + }, + { + "key": "ep", + "title": "Epitope mutations", + "type": "continuous" + }, + { + "key": "ne", + "title": "Non-epitope mutations", + "type": "continuous" + }, + { + "key": "glyc", + "title": "Glycosylation changes", + "type": "continuous" + }, + { + "key": "region", + "title": "Region", + "type": "categorical" + }, + { + "key": "country", + "title": "Country", + "type": "categorical" + }, + { + "key": "division", + "title": "Division", + "type": "categorical" + }, + { + "key": "accession_ha", + "title": "Accession (HA)", + "type": "categorical" + }, + { + "key": "accession_na", + "title": "Accession (NA)", + "type": "categorical" + }, + { + "key": "submitting_lab", + "title": "Submitting lab", + "type": "categorical" + }, + { + "key": "originating_lab", + "title": "Originating lab", + "type": "categorical" + }, + { + "key": "recency", + "title": "Submission date", + "type": "ordinal" + }, + { + "key": "epiweek", + "title": "Epiweek (CDC)", + "type": "ordinal" + }, + { + "key": "year_month", + "title": "Year/month", + "type": "categorical" + }, + { + "key": "tsne_x", + "title": "t-SNE 1", + "type": "continuous" + }, + { + "key": "tsne_y", + "title": "t-SNE 2", + "type": "continuous" + }, + { + "key": "tsne_cluster", + "title": "t-SNE cluster", + "type": "categorical" + } + ], + "geo_resolutions": [ + "division", + "country", + "region" + ], + "display_defaults": { + "map_triplicate": true, + "color_by": "clade_membership" + }, + "filters": [ + "clade_membership", + "subclade", + "region", + "country", + "division", + "submitting_lab", + "recency", + "epiweek", + "year_month", + "tsne_cluster" + ], + "panels": [ + "tree", + "map", + "entropy", + "frequencies" + ] +} diff --git a/config/h3n2/ha/auspice_config.json b/config/h3n2/ha/auspice_config.json new file mode 100644 index 00000000..1d7a787a --- /dev/null +++ b/config/h3n2/ha/auspice_config.json @@ -0,0 +1,221 @@ +{ + "title": "Real-time tracking of influenza A/H3N2 evolution", + "maintainers": [ + { + "name": "Jennifer Chang", + "url": "https://bedford.io/team/jennifer-chang/" + }, + { + "name": "Jover Lee", + "url": "https://bedford.io/team/jover-lee/" + }, + { + "name": "John Huddleston", + "url": "https://bedford.io/team/john-huddleston/" + }, + { + "name": "Richard Neher", + "url": "https://neherlab.org/richard-neher.html" + }, + { + "name": "Trevor Bedford", + "url": "https://bedford.io/team/trevor-bedford/" + } + ], + "data_provenance": [ + { + "name": "GISAID" + } + ], + "build_url": "https://github.com/nextstrain/seasonal-flu", + "colorings": [ + { + "key": "gt", + "title": "Genotype", + "type": "categorical" + }, + { + "key": "num_date", + "title": "Date", + "type": "continuous" + }, + { + "key": "clade_membership", + "title": "Clade", + "type": "categorical" + }, + { + "key": "subclade", + "title": "Subclade", + "type": "categorical", + "scale": [ + [ + "G.1.3.1", + "#447CCD" + ], + [ + "J", + "#5EA9A1" + ], + [ + "J.1", + "#8ABB6A" + ], + [ + "J.2", + "#BEBB48" + ], + [ + "J.3", + "#E29E39" + ], + [ + "J.4", + "#E2562B" + ] + ] + }, + { + "key": "haplotype", + "title": "Derived haplotype", + "type": "categorical" + }, + { + "key": "ne_star", + "title": "Mutational load", + "type": "continuous" + }, + { + "key": "cTiter", + "title": "Antigenic advance (tree model)", + "type": "continuous" + }, + { + "key": "cTiterSub", + "title": "Antigenic advance (sub model)", + "type": "continuous" + }, + { + "key": "cTiter_x", + "title": "HI antigenic novelty", + "type": "continuous" + }, + { + "key": "lbi", + "title": "Local branching index", + "type": "continuous" + }, + { + "key": "ep", + "title": "Epitope mutations", + "type": "continuous" + }, + { + "key": "ne", + "title": "Non-epitope mutations", + "type": "continuous" + }, + { + "key": "rb", + "title": "RBS adjacent mutations", + "type": "continuous" + }, + { + "key": "glyc", + "title": "Glycosylation changes", + "type": "continuous" + }, + { + "key": "region", + "title": "Region", + "type": "categorical" + }, + { + "key": "country", + "title": "Country", + "type": "categorical" + }, + { + "key": "division", + "title": "Division", + "type": "categorical" + }, + { + "key": "accession_ha", + "title": "Accession (HA)", + "type": "categorical" + }, + { + "key": "accession_na", + "title": "Accession (NA)", + "type": "categorical" + }, + { + "key": "submitting_lab", + "title": "Submitting lab", + "type": "categorical" + }, + { + "key": "originating_lab", + "title": "Originating lab", + "type": "categorical" + }, + { + "key": "recency", + "title": "Submission date", + "type": "ordinal" + }, + { + "key": "epiweek", + "title": "Epiweek (CDC)", + "type": "ordinal" + }, + { + "key": "year_month", + "title": "Year/month", + "type": "categorical" + }, + { + "key": "tsne_x", + "title": "t-SNE 1", + "type": "continuous" + }, + { + "key": "tsne_y", + "title": "t-SNE 2", + "type": "continuous" + }, + { + "key": "tsne_cluster", + "title": "t-SNE cluster", + "type": "categorical" + } + ], + "geo_resolutions": [ + "division", + "country", + "region" + ], + "display_defaults": { + "map_triplicate": true, + "color_by": "clade_membership" + }, + "filters": [ + "clade_membership", + "subclade", + "region", + "country", + "division", + "submitting_lab", + "recency", + "epiweek", + "year_month", + "tsne_cluster" + ], + "panels": [ + "tree", + "map", + "entropy", + "frequencies" + ] +} diff --git a/config/h3n2/na/auspice_config.json b/config/h3n2/na/auspice_config.json new file mode 100644 index 00000000..5cc55ded --- /dev/null +++ b/config/h3n2/na/auspice_config.json @@ -0,0 +1,193 @@ +{ + "title": "Real-time tracking of influenza A/H3N2 evolution", + "maintainers": [ + { + "name": "Jennifer Chang", + "url": "https://bedford.io/team/jennifer-chang/" + }, + { + "name": "Jover Lee", + "url": "https://bedford.io/team/jover-lee/" + }, + { + "name": "John Huddleston", + "url": "https://bedford.io/team/john-huddleston/" + }, + { + "name": "Richard Neher", + "url": "https://neherlab.org/richard-neher.html" + }, + { + "name": "Trevor Bedford", + "url": "https://bedford.io/team/trevor-bedford/" + } + ], + "data_provenance": [ + { + "name": "GISAID" + } + ], + "build_url": "https://github.com/nextstrain/seasonal-flu", + "colorings": [ + { + "key": "gt", + "title": "Genotype", + "type": "categorical" + }, + { + "key": "num_date", + "title": "Date", + "type": "continuous" + }, + { + "key": "clade_membership", + "title": "Clade", + "type": "categorical" + }, + { + "key": "subclade", + "title": "Subclade", + "type": "categorical", + "scale": [ + [ + "B.4", + "#4A8CC2" + ], + [ + "B.4.1", + "#71B486" + ], + [ + "B.4.2", + "#ABBD52" + ], + [ + "B.4.3", + "#DEA73C" + ] + ] + }, + { + "key": "haplotype", + "title": "Derived haplotype", + "type": "categorical" + }, + { + "key": "ne_star", + "title": "Mutational load", + "type": "continuous" + }, + { + "key": "lbi", + "title": "Local branching index", + "type": "continuous" + }, + { + "key": "ep", + "title": "Epitope mutations", + "type": "continuous" + }, + { + "key": "ne", + "title": "Non-epitope mutations", + "type": "continuous" + }, + { + "key": "glyc", + "title": "Glycosylation changes", + "type": "continuous" + }, + { + "key": "region", + "title": "Region", + "type": "categorical" + }, + { + "key": "country", + "title": "Country", + "type": "categorical" + }, + { + "key": "division", + "title": "Division", + "type": "categorical" + }, + { + "key": "accession_ha", + "title": "Accession (HA)", + "type": "categorical" + }, + { + "key": "accession_na", + "title": "Accession (NA)", + "type": "categorical" + }, + { + "key": "submitting_lab", + "title": "Submitting lab", + "type": "categorical" + }, + { + "key": "originating_lab", + "title": "Originating lab", + "type": "categorical" + }, + { + "key": "recency", + "title": "Submission date", + "type": "ordinal" + }, + { + "key": "epiweek", + "title": "Epiweek (CDC)", + "type": "ordinal" + }, + { + "key": "year_month", + "title": "Year/month", + "type": "categorical" + }, + { + "key": "tsne_x", + "title": "t-SNE 1", + "type": "continuous" + }, + { + "key": "tsne_y", + "title": "t-SNE 2", + "type": "continuous" + }, + { + "key": "tsne_cluster", + "title": "t-SNE cluster", + "type": "categorical" + } + ], + "geo_resolutions": [ + "division", + "country", + "region" + ], + "display_defaults": { + "map_triplicate": true, + "color_by": "clade_membership" + }, + "filters": [ + "clade_membership", + "subclade", + "region", + "country", + "division", + "submitting_lab", + "recency", + "epiweek", + "year_month", + "tsne_cluster" + ], + "panels": [ + "tree", + "map", + "entropy", + "frequencies" + ] +} diff --git a/config/vic/ha/auspice_config.json b/config/vic/ha/auspice_config.json new file mode 100644 index 00000000..e2fccd11 --- /dev/null +++ b/config/vic/ha/auspice_config.json @@ -0,0 +1,200 @@ +{ + "title": "Real-time tracking of influenza B/Vic evolution", + "maintainers": [ + { + "name": "Jennifer Chang", + "url": "https://bedford.io/team/jennifer-chang/" + }, + { + "name": "Jover Lee", + "url": "https://bedford.io/team/jover-lee/" + }, + { + "name": "John Huddleston", + "url": "https://bedford.io/team/john-huddleston/" + }, + { + "name": "Richard Neher", + "url": "https://neherlab.org/richard-neher.html" + }, + { + "name": "Trevor Bedford", + "url": "https://bedford.io/team/trevor-bedford/" + } + ], + "data_provenance": [ + { + "name": "GISAID" + } + ], + "build_url": "https://github.com/nextstrain/seasonal-flu", + "colorings": [ + { + "key": "gt", + "title": "Genotype", + "type": "categorical" + }, + { + "key": "num_date", + "title": "Date", + "type": "continuous" + }, + { + "key": "clade_membership", + "title": "Clade", + "type": "categorical" + }, + { + "key": "subclade", + "title": "Subclade", + "type": "categorical", + "scale": [ + [ + "C.2", + "#4272CE" + ], + [ + "C.3", + "#58A2AC" + ], + [ + "C.5", + "#7DB877" + ], + [ + "C.5.1", + "#AEBD50" + ], + [ + "C.5.4", + "#D8AE3E" + ], + [ + "C.5.6", + "#E67A32" + ], + [ + "C.5.7", + "#DB2823" + ] + ] + }, + { + "key": "cTiter", + "title": "Antigenic advance (tree model)", + "type": "continuous" + }, + { + "key": "cTiterSub", + "title": "Antigenic advance (sub model)", + "type": "continuous" + }, + { + "key": "cTiter_x", + "title": "HI antigenic novelty", + "type": "continuous" + }, + { + "key": "lbi", + "title": "Local branching index", + "type": "continuous" + }, + { + "key": "glyc", + "title": "Glycosylation changes", + "type": "continuous" + }, + { + "key": "region", + "title": "Region", + "type": "categorical" + }, + { + "key": "country", + "title": "Country", + "type": "categorical" + }, + { + "key": "division", + "title": "Division", + "type": "categorical" + }, + { + "key": "accession_ha", + "title": "Accession (HA)", + "type": "categorical" + }, + { + "key": "accession_na", + "title": "Accession (NA)", + "type": "categorical" + }, + { + "key": "submitting_lab", + "title": "Submitting lab", + "type": "categorical" + }, + { + "key": "originating_lab", + "title": "Originating lab", + "type": "categorical" + }, + { + "key": "recency", + "title": "Submission date", + "type": "ordinal" + }, + { + "key": "epiweek", + "title": "Epiweek (CDC)", + "type": "ordinal" + }, + { + "key": "year_month", + "title": "Year/month", + "type": "categorical" + }, + { + "key": "tsne_x", + "title": "t-SNE 1", + "type": "continuous" + }, + { + "key": "tsne_y", + "title": "t-SNE 2", + "type": "continuous" + }, + { + "key": "tsne_cluster", + "title": "t-SNE cluster", + "type": "categorical" + } + ], + "geo_resolutions": [ + "division", + "country", + "region" + ], + "display_defaults": { + "map_triplicate": true, + "color_by": "clade_membership" + }, + "filters": [ + "clade_membership", + "subclade", + "region", + "country", + "division", + "submitting_lab", + "recency", + "epiweek", + "year_month", + "tsne_cluster" + ], + "panels": [ + "tree", + "map", + "entropy", + "frequencies" + ] +} diff --git a/config/vic/na/auspice_config.json b/config/vic/na/auspice_config.json new file mode 100644 index 00000000..f877353a --- /dev/null +++ b/config/vic/na/auspice_config.json @@ -0,0 +1,193 @@ +{ + "title": "Real-time tracking of influenza B/Vic evolution", + "maintainers": [ + { + "name": "Jennifer Chang", + "url": "https://bedford.io/team/jennifer-chang/" + }, + { + "name": "Jover Lee", + "url": "https://bedford.io/team/jover-lee/" + }, + { + "name": "John Huddleston", + "url": "https://bedford.io/team/john-huddleston/" + }, + { + "name": "Richard Neher", + "url": "https://neherlab.org/richard-neher.html" + }, + { + "name": "Trevor Bedford", + "url": "https://bedford.io/team/trevor-bedford/" + } + ], + "data_provenance": [ + { + "name": "GISAID" + } + ], + "build_url": "https://github.com/nextstrain/seasonal-flu", + "colorings": [ + { + "key": "gt", + "title": "Genotype", + "type": "categorical" + }, + { + "key": "num_date", + "title": "Date", + "type": "continuous" + }, + { + "key": "clade_membership", + "title": "Clade", + "type": "categorical" + }, + { + "key": "subclade", + "title": "Subclade", + "type": "categorical", + "scale": [ + [ + "B", + "#3E5DD0" + ], + [ + "B.3", + "#4A8CC2" + ], + [ + "B.5", + "#60AA9E" + ], + [ + "B.6", + "#80B974" + ], + [ + "B.7", + "#A6BE55" + ], + [ + "B.7.1", + "#CBB742" + ], + [ + "B.7.2", + "#E29D39" + ], + [ + "B.7.3", + "#E56A2F" + ], + [ + "B.8", + "#DB2823" + ] + ] + }, + { + "key": "lbi", + "title": "Local branching index", + "type": "continuous" + }, + { + "key": "glyc", + "title": "Glycosylation changes", + "type": "continuous" + }, + { + "key": "region", + "title": "Region", + "type": "categorical" + }, + { + "key": "country", + "title": "Country", + "type": "categorical" + }, + { + "key": "division", + "title": "Division", + "type": "categorical" + }, + { + "key": "accession_ha", + "title": "Accession (HA)", + "type": "categorical" + }, + { + "key": "accession_na", + "title": "Accession (NA)", + "type": "categorical" + }, + { + "key": "submitting_lab", + "title": "Submitting lab", + "type": "categorical" + }, + { + "key": "originating_lab", + "title": "Originating lab", + "type": "categorical" + }, + { + "key": "recency", + "title": "Submission date", + "type": "ordinal" + }, + { + "key": "epiweek", + "title": "Epiweek (CDC)", + "type": "ordinal" + }, + { + "key": "year_month", + "title": "Year/month", + "type": "categorical" + }, + { + "key": "tsne_x", + "title": "t-SNE 1", + "type": "continuous" + }, + { + "key": "tsne_y", + "title": "t-SNE 2", + "type": "continuous" + }, + { + "key": "tsne_cluster", + "title": "t-SNE cluster", + "type": "categorical" + } + ], + "geo_resolutions": [ + "division", + "country", + "region" + ], + "display_defaults": { + "map_triplicate": true, + "color_by": "clade_membership" + }, + "filters": [ + "clade_membership", + "subclade", + "region", + "country", + "division", + "submitting_lab", + "recency", + "epiweek", + "year_month", + "tsne_cluster" + ], + "panels": [ + "tree", + "map", + "entropy", + "frequencies" + ] +} diff --git a/profiles/nextflu-private.yaml b/profiles/nextflu-private.yaml index 7763ba59..7fb770b0 100644 --- a/profiles/nextflu-private.yaml +++ b/profiles/nextflu-private.yaml @@ -169,101 +169,11 @@ builds: data: "data/vic/who_ferret_egg_hi_titers.tsv" prefix: egg_hi_ title: "Egg-passaged HI titers from ferret sera" - subsamples: *titers-subsampling-scheme - # Define builds with representative sampling for cases when we need to - # minimize sampling bias (e.g., LBI, tree topology, frequencies, etc.). - 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" - subclades: "config/h1n1pdm/{segment}/subclades.tsv" - auspice_config: "profiles/nextflu-private/h1n1pdm/{segment}/auspice_config.json" - vaccines: "config/h1n1pdm/vaccine.json" - enable_glycosylation: true - enable_lbi: true - enable_titer_models: true - enable_measurements: true - enable_embeddings: true - min_date: "2Y" - reference_min_date: "6Y" - max_date: "4W" - include: "config/h1n1pdm/reference_strains.txt" - exclude: "config/h1n1pdm/outliers.txt" - titer_collections: - - name: cell_hi - data: "data/h1n1pdm/who_ferret_cell_hi_titers.tsv" - prefix: cell_hi_ - title: "Cell-passaged HI titers from ferret sera" - 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 2700 --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 300 --min-date {min_date} --exclude {exclude} - priorities: "titers" - references: - filters: --query "(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/clades.tsv" - subclades: "config/h3n2/{segment}/subclades.tsv" - auspice_config: "profiles/nextflu-private/h3n2/{segment}/auspice_config.json" - vaccines: "config/h3n2/vaccine.json" - enable_glycosylation: true - enable_lbi: true - enable_forecasts: true - enable_titer_models: true - enable_measurements: true - enable_embeddings: true - min_date: "2Y" - reference_min_date: "6Y" - max_date: "4W" - include: "config/h3n2/reference_strains.txt" - exclude: "config/h3n2/outliers.txt" - titer_collections: - - name: cell_fra - data: "data/h3n2/who_ferret_cell_fra_titers.tsv" - prefix: cell_fra_ - title: "Cell-passaged FRA titers from ferret sera" - - name: human_cell_fra - data: "data/h3n2/who_human_cell_fra_titers.tsv" - prefix: human_cell_fra_ - title: "Cell-passaged FRA titers from pooled human sera" - 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" - subclades: "config/vic/{segment}/subclades.tsv" - auspice_config: "profiles/nextflu-private/vic/{segment}/auspice_config.json" - vaccines: "config/vic/vaccine.json" - enable_glycosylation: true - enable_lbi: true - enable_titer_models: true - enable_measurements: true - enable_embeddings: true - min_date: "2Y" - reference_min_date: "6Y" - max_date: "4W" - include: "config/vic/reference_strains.txt" - exclude: "config/vic/outliers.txt" - titer_collections: - - name: cell_hi - data: "data/vic/who_ferret_cell_hi_titers.tsv" - prefix: cell_hi_ - title: "Cell-passaged HI titers from ferret sera" - name: human_cell_hi data: "data/vic/who_human_cell_hi_titers.tsv" prefix: human_cell_hi_ title: "Cell-passaged HI titers from pooled human sera" - subsamples: *representative-subsampling-scheme + subsamples: *titers-subsampling-scheme fitness_model: models: diff --git a/profiles/nextstrain-public.yaml b/profiles/nextstrain-public.yaml index efc5d5d4..dd124154 100644 --- a/profiles/nextstrain-public.yaml +++ b/profiles/nextstrain-public.yaml @@ -97,7 +97,24 @@ array-builds: resolution: - 2y build_name: "seasonal-flu_{lineage}_2y" - build_params: *shared-hi-build-params + build_params: + auspice_name: "seasonal-flu_{lineage}_{{segment}}_{resolution}" + 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" + subclades: "config/{lineage}/{{segment}}/subclades.tsv" + auspice_config: "config/{lineage}/{{segment}}/auspice_config.json" + vaccines: "config/{lineage}/vaccine.json" + enable_glycosylation: true + enable_lbi: true + enable_titer_models: true + enable_embeddings: true + include: "'config/{lineage}/reference_strains.txt'" + exclude: "'config/{lineage}/outliers.txt'" + titer_collections: + - name: cdc_cell_hi + data: "data/{lineage}/cdc_ferret_cell_hi_titers.tsv" subsamples: *subsampling-scheme 3Y-hi-builds: patterns: @@ -188,7 +205,7 @@ array-builds: tree_exclude_sites: "config/{lineage}/{{segment}}/exclude-sites.txt" clades: "config/{lineage}/ha/clades.tsv" subclades: "config/{lineage}/{{segment}}/subclades.tsv" - auspice_config: "config/{lineage}/auspice_config.json" + auspice_config: "config/{lineage}/{{segment}}/auspice_config.json" vaccines: "config/{lineage}/vaccine.json" enable_glycosylation: true enable_lbi: true