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Merge pull request #106 from nextstrain/update-24C
Add clade definition for 24C
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,147 +1,147 @@ | ||
| # See ingest/README.md for all available data | ||
| data_provenances: | ||
| - gisaid | ||
| - open | ||
| variant_classifications: | ||
| - nextstrain_clades | ||
| - pango_lineages | ||
| geo_resolutions: | ||
| - global | ||
|
|
||
| # Params for the prepare data scripts | ||
| # Define params for each data_provenance / variant_classification / geo_resolution combination | ||
| # Include `max_date` if you don't want to use today as the max date | ||
| prepare_data: | ||
| gisaid: | ||
| nextstrain_clades: | ||
| global: | ||
| included_days: 150 | ||
| location_min_seq: 50 | ||
| location_min_seq_days: 30 | ||
| excluded_locations: "defaults/global_excluded_locations.txt" | ||
| prune_seq_days: 12 | ||
| clade_min_seq: 2000 | ||
| clade_min_seq_days: 150 | ||
| pango_lineages: | ||
| global: | ||
| included_days: 150 | ||
| location_min_seq: 150 | ||
| location_min_seq_days: 30 | ||
| excluded_locations: "defaults/global_excluded_locations.txt" | ||
| prune_seq_days: 12 | ||
| clade_min_seq: 1 | ||
| clade_min_seq_days: 150 | ||
| collapse_threshold: 350 | ||
| open: | ||
| nextstrain_clades: | ||
| global: | ||
| included_days: 150 | ||
| location_min_seq: 50 | ||
| location_min_seq_days: 30 | ||
| excluded_locations: "defaults/global_excluded_locations.txt" | ||
| prune_seq_days: 12 | ||
| clade_min_seq: 2000 | ||
| clade_min_seq_days: 150 | ||
| pango_lineages: | ||
| global: | ||
| included_days: 150 | ||
| location_min_seq: 150 | ||
| location_min_seq_days: 30 | ||
| excluded_locations: "defaults/global_excluded_locations.txt" | ||
| prune_seq_days: 12 | ||
| clade_min_seq: 1 | ||
| clade_min_seq_days: 150 | ||
| collapse_threshold: 350 | ||
|
|
||
| # Params for the model run scripts | ||
| models: | ||
| gisaid: | ||
| nextstrain_clades: | ||
| global: | ||
| pivot: "24A" | ||
| pango_lineages: | ||
| global: | ||
| pivot: "JN.1" | ||
| open: | ||
| nextstrain_clades: | ||
| global: | ||
| pivot: "24A" | ||
| pango_lineages: | ||
| global: | ||
| pivot: "JN.1" | ||
|
|
||
| # Model configs | ||
| mlr_config: "config/mlr-config.yaml" | ||
| # don't run renewal model by default | ||
| #renewal_config: "config/renewal-config.yaml" | ||
|
|
||
|
|
||
| # A mapping between nextstrain clades, defining pango lineages and clade colours. | ||
| # Colours will be assigned to pango lineages by first associating it with its | ||
| # corresponding nextstrain clade and then interpolating colours close to the | ||
| # clade's colour; this allows each individual lineage to have its own colour | ||
| # whilst being able to visually associate them back to their nextstrain clade. | ||
| # | ||
| # The order in the list must be hierarchical w.r.t pango lineages, i.e. XBB.1.9 | ||
| # must appear _before_ XBB | ||
| # | ||
| # NOTES: | ||
| # * Lineages are ordered (in the legend & for the GA estimates) alphabetically | ||
| # via their full pango name. This doesn't map nicely onto nextstrain clade | ||
| # definitions, which is why an individual colour scale defined here may appear | ||
| # in multiple parts of the graph. | ||
| # * Lineages which are not a descendant of a clade-defining lineage will be | ||
| # grouped as 'other' | ||
| clade_definitions: | ||
| - clade: "24B" | ||
| display_name: "24B (JN.1.11.1)" | ||
| defining_lineage: "JN.1.11.1" | ||
| color: '#DC2F24' | ||
| - clade: "24A" | ||
| display_name: "24A (JN.1)" | ||
| defining_lineage: "JN.1" | ||
| color: '#E4632E' | ||
| - clade: "23I" | ||
| display_name: "23I (BA.2.86)" | ||
| defining_lineage: "BA.2.86" | ||
| color: '#E69136' | ||
| - clade: "23H" | ||
| display_name: "23H (HK.3)" | ||
| defining_lineage: "HK.3" | ||
| color: '#D9AD3D' | ||
| - clade: "23G" | ||
| display_name: "23G (XBB.1.5.70)" | ||
| defining_lineage: "XBB.1.5.70" | ||
| color: '#C1BA47' | ||
| - clade: "23F" | ||
| display_name: "23F (EG.5.1)" | ||
| defining_lineage: "EG.5.1" | ||
| color: '#A2BE57' | ||
| - clade: "23E" | ||
| display_name: "23E (XBB.2.3)" | ||
| defining_lineage: "XBB.2.3" | ||
| color: '#83BA70' | ||
| - clade: "23D" | ||
| display_name: "23D (XBB.1.9)" | ||
| defining_lineage: "XBB.1.9" | ||
| color: '#69B091' | ||
| - clade: "23C" | ||
| display_name: "23C (CH.1.1)" | ||
| defining_lineage: "CH.1.1" | ||
| color: '#549DB2' | ||
| - clade: "23B" | ||
| display_name: "23B (XBB.1.16)" | ||
| defining_lineage: "XBB.1.16" | ||
| color: '#4580CA' | ||
| - clade: "22F" | ||
| display_name: "22F (XBB)" | ||
| defining_lineage: "XBB" | ||
| color: '#3E58CF' | ||
| - clade: "23A" | ||
| display_name: "23A (XBB.1.5)" | ||
| defining_lineage: "XBB.1.5" | ||
| color: '#462EB9' | ||
| - clade: "other" | ||
| display_name: "other" | ||
| defining_lineage: False | ||
| color: '#777777' | ||
| # See ingest/README.md for all available data | ||
| data_provenances: | ||
| - gisaid | ||
| - open | ||
| variant_classifications: | ||
| - nextstrain_clades | ||
| - pango_lineages | ||
| geo_resolutions: | ||
| - global | ||
|
|
||
| # Params for the prepare data scripts | ||
| # Define params for each data_provenance / variant_classification / geo_resolution combination | ||
| # Include `max_date` if you don't want to use today as the max date | ||
| prepare_data: | ||
| gisaid: | ||
| nextstrain_clades: | ||
| global: | ||
| included_days: 150 | ||
| location_min_seq: 50 | ||
| location_min_seq_days: 30 | ||
| excluded_locations: "defaults/global_excluded_locations.txt" | ||
| prune_seq_days: 12 | ||
| clade_min_seq: 2000 | ||
| clade_min_seq_days: 150 | ||
| pango_lineages: | ||
| global: | ||
| included_days: 150 | ||
| location_min_seq: 150 | ||
| location_min_seq_days: 30 | ||
| excluded_locations: "defaults/global_excluded_locations.txt" | ||
| prune_seq_days: 12 | ||
| clade_min_seq: 1 | ||
| clade_min_seq_days: 150 | ||
| collapse_threshold: 350 | ||
| open: | ||
| nextstrain_clades: | ||
| global: | ||
| included_days: 150 | ||
| location_min_seq: 50 | ||
| location_min_seq_days: 30 | ||
| excluded_locations: "defaults/global_excluded_locations.txt" | ||
| prune_seq_days: 12 | ||
| clade_min_seq: 2000 | ||
| clade_min_seq_days: 150 | ||
| pango_lineages: | ||
| global: | ||
| included_days: 150 | ||
| location_min_seq: 150 | ||
| location_min_seq_days: 30 | ||
| excluded_locations: "defaults/global_excluded_locations.txt" | ||
| prune_seq_days: 12 | ||
| clade_min_seq: 1 | ||
| clade_min_seq_days: 150 | ||
| collapse_threshold: 350 | ||
|
|
||
| # Params for the model run scripts | ||
| models: | ||
| gisaid: | ||
| nextstrain_clades: | ||
| global: | ||
| pivot: "24A" | ||
| pango_lineages: | ||
| global: | ||
| pivot: "JN.1" | ||
| open: | ||
| nextstrain_clades: | ||
| global: | ||
| pivot: "24A" | ||
| pango_lineages: | ||
| global: | ||
| pivot: "JN.1" | ||
|
|
||
| # Model configs | ||
| mlr_config: "config/mlr-config.yaml" | ||
| # don't run renewal model by default | ||
| #renewal_config: "config/renewal-config.yaml" | ||
|
|
||
|
|
||
| # A mapping between nextstrain clades, defining pango lineages and clade colours. | ||
| # Colours will be assigned to pango lineages by first associating it with its | ||
| # corresponding nextstrain clade and then interpolating colours close to the | ||
| # clade's colour; this allows each individual lineage to have its own colour | ||
| # whilst being able to visually associate them back to their nextstrain clade. | ||
| # | ||
| # The order in the list must be hierarchical w.r.t pango lineages, i.e. XBB.1.9 | ||
| # must appear _before_ XBB | ||
| # | ||
| # NOTES: | ||
| # * Lineages are ordered (in the legend & for the GA estimates) alphabetically | ||
| # via their full pango name. This doesn't map nicely onto nextstrain clade | ||
| # definitions, which is why an individual colour scale defined here may appear | ||
| # in multiple parts of the graph. | ||
| # * Lineages which are not a descendant of a clade-defining lineage will be | ||
| # grouped as 'other' | ||
| clade_definitions: | ||
| - clade: "24C" | ||
| display_name: "24C (KP.3)" | ||
| defining_lineage: "KP.3" | ||
| color: '#DC2F24' | ||
| - clade: "24B" | ||
| display_name: "24B (JN.1.11.1)" | ||
| defining_lineage: "JN.1.11.1" | ||
| color: '#E4632E' | ||
| - clade: "24A" | ||
| display_name: "24A (JN.1)" | ||
| defining_lineage: "JN.1" | ||
| color: '#E69136' | ||
| - clade: "23I" | ||
| display_name: "23I (BA.2.86)" | ||
| defining_lineage: "BA.2.86" | ||
| color: '#D9AD3D' | ||
| - clade: "23H" | ||
| display_name: "23H (HK.3)" | ||
| defining_lineage: "HK.3" | ||
| color: '#C1BA47' | ||
| - clade: "23G" | ||
| display_name: "23G (XBB.1.5.70)" | ||
| defining_lineage: "XBB.1.5.70" | ||
| color: '#A2BE57' | ||
| - clade: "23F" | ||
| display_name: "23F (EG.5.1)" | ||
| defining_lineage: "EG.5.1" | ||
| color: '#83BA70' | ||
| - clade: "23E" | ||
| display_name: "23E (XBB.2.3)" | ||
| defining_lineage: "XBB.2.3" | ||
| color: '#69B091' | ||
| - clade: "23D" | ||
| display_name: "23D (XBB.1.9)" | ||
| defining_lineage: "XBB.1.9" | ||
| color: '#549DB2' | ||
| - clade: "23C" | ||
| display_name: "23C (CH.1.1)" | ||
| defining_lineage: "CH.1.1" | ||
| color: '#4580CA' | ||
| - clade: "23B" | ||
| display_name: "23B (XBB.1.16)" | ||
| defining_lineage: "XBB.1.16" | ||
| color: '#3E58CF' | ||
| - clade: "22F" | ||
| display_name: "22F (XBB)" | ||
| defining_lineage: "XBB" | ||
| color: '#462EB9' | ||
| - clade: "other" | ||
| display_name: "other" | ||
| defining_lineage: False | ||
| color: '#777777' |