From 70aa38b09871c2638a024485369e7c6704ec1c55 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Thu, 18 Jul 2024 10:54:50 -0700 Subject: [PATCH] Convert config.yaml to LF line endings --- config/config.yaml | 294 ++++++++++++++++++++++----------------------- 1 file changed, 147 insertions(+), 147 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index acde281..b711c6a 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -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: "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'