diff --git a/config/h1n1pdm/auspice_config.json b/config/h1n1pdm/auspice_config.json index 2c049bef..1b4f1759 100644 --- a/config/h1n1pdm/auspice_config.json +++ b/config/h1n1pdm/auspice_config.json @@ -158,5 +158,16 @@ "metadata_columns": [ "accession_ha", "accession_na" - ] -} + ], + "extensions": { + "nextclade": { + "clade_node_attrs": [ + { + "name": "subclade", + "displayName": "Subclade", + "description": "Experimental fine-grained subclade annotation." + } + ] + } + } +} \ No newline at end of file diff --git a/config/h1n1pdm/ha/auspice_config.json b/config/h1n1pdm/ha/auspice_config.json index fbf545b9..dd58f4d9 100644 --- a/config/h1n1pdm/ha/auspice_config.json +++ b/config/h1n1pdm/ha/auspice_config.json @@ -263,5 +263,16 @@ "gisaid_strain", "accession_ha", "accession_na" - ] -} + ], + "extensions": { + "nextclade": { + "clade_node_attrs": [ + { + "name": "subclade", + "displayName": "Subclade", + "description": "Experimental fine-grained subclade annotation." + } + ] + } + } +} \ No newline at end of file diff --git a/config/h1n1pdm/na/auspice_config.json b/config/h1n1pdm/na/auspice_config.json index 8eb3865c..90db2a03 100644 --- a/config/h1n1pdm/na/auspice_config.json +++ b/config/h1n1pdm/na/auspice_config.json @@ -196,5 +196,16 @@ "gisaid_strain", "accession_ha", "accession_na" - ] -} + ], + "extensions": { + "nextclade": { + "clade_node_attrs": [ + { + "name": "subclade", + "displayName": "Subclade", + "description": "Experimental fine-grained subclade annotation." + } + ] + } + } +} \ No newline at end of file diff --git a/config/h3n2/auspice_config.json b/config/h3n2/auspice_config.json index 0f4016f1..83e9e40e 100644 --- a/config/h3n2/auspice_config.json +++ b/config/h3n2/auspice_config.json @@ -168,5 +168,16 @@ "metadata_columns": [ "accession_ha", "accession_na" - ] -} + ], + "extensions": { + "nextclade": { + "clade_node_attrs": [ + { + "name": "subclade", + "displayName": "Subclade", + "description": "Experimental fine-grained subclade annotation." + } + ] + } + } +} \ No newline at end of file diff --git a/config/h3n2/ha/auspice_config.json b/config/h3n2/ha/auspice_config.json index bc473236..93f6d0d5 100644 --- a/config/h3n2/ha/auspice_config.json +++ b/config/h3n2/ha/auspice_config.json @@ -253,5 +253,16 @@ "gisaid_strain", "accession_ha", "accession_na" - ] -} + ], + "extensions": { + "nextclade": { + "clade_node_attrs": [ + { + "name": "subclade", + "displayName": "Subclade", + "description": "Experimental fine-grained subclade annotation." + } + ] + } + } +} \ No newline at end of file diff --git a/config/h3n2/na/auspice_config.json b/config/h3n2/na/auspice_config.json index 19d164ac..44eb3b1e 100644 --- a/config/h3n2/na/auspice_config.json +++ b/config/h3n2/na/auspice_config.json @@ -209,5 +209,16 @@ "gisaid_strain", "accession_ha", "accession_na" - ] -} + ], + "extensions": { + "nextclade": { + "clade_node_attrs": [ + { + "name": "subclade", + "displayName": "Subclade", + "description": "Experimental fine-grained subclade annotation." + } + ] + } + } +} \ No newline at end of file diff --git a/config/vic/auspice_config.json b/config/vic/auspice_config.json index f86f95f4..4e01915e 100644 --- a/config/vic/auspice_config.json +++ b/config/vic/auspice_config.json @@ -143,5 +143,16 @@ "metadata_columns": [ "accession_ha", "accession_na" - ] -} + ], + "extensions": { + "nextclade": { + "clade_node_attrs": [ + { + "name": "subclade", + "displayName": "Subclade", + "description": "Experimental fine-grained subclade annotation." + } + ] + } + } +} \ No newline at end of file diff --git a/config/vic/ha/auspice_config.json b/config/vic/ha/auspice_config.json index ff882a89..e49e85c4 100644 --- a/config/vic/ha/auspice_config.json +++ b/config/vic/ha/auspice_config.json @@ -228,5 +228,16 @@ "gisaid_strain", "accession_ha", "accession_na" - ] -} + ], + "extensions": { + "nextclade": { + "clade_node_attrs": [ + { + "name": "subclade", + "displayName": "Subclade", + "description": "Experimental fine-grained subclade annotation." + } + ] + } + } +} \ No newline at end of file diff --git a/config/vic/na/auspice_config.json b/config/vic/na/auspice_config.json index d31f2844..02636518 100644 --- a/config/vic/na/auspice_config.json +++ b/config/vic/na/auspice_config.json @@ -221,5 +221,16 @@ "gisaid_strain", "accession_ha", "accession_na" - ] -} + ], + "extensions": { + "nextclade": { + "clade_node_attrs": [ + { + "name": "subclade", + "displayName": "Subclade", + "description": "Experimental fine-grained subclade annotation." + } + ] + } + } +} \ No newline at end of file diff --git a/profiles/ci/builds.yaml b/profiles/ci/builds.yaml index d9abe4fa..0f577c56 100644 --- a/profiles/ci/builds.yaml +++ b/profiles/ci/builds.yaml @@ -50,6 +50,7 @@ builds: 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" min_date: "12Y" auspice_config: "config/h3n2/auspice_config.json" enable_titer_models: true