From afe2cd915b226d84046e9ff5d3c34a9ecc730a45 Mon Sep 17 00:00:00 2001 From: John Huddleston Date: Mon, 18 Nov 2024 13:47:11 -0800 Subject: [PATCH] Add Nextclade extension to public builds Adds Nextclade extension with "subclade" annotation to Auspice config for all public builds, allowing users to get these subclade annotations from Nextclade for any public tree. To test this functionality, I added subclade annotations to the CI build and confirmed that the extension worked as expected by uploading the CI Auspice JSON to the staging server before and after I included the extension in the JSON. --- config/h1n1pdm/auspice_config.json | 15 +++++++++++++-- config/h1n1pdm/ha/auspice_config.json | 15 +++++++++++++-- config/h1n1pdm/na/auspice_config.json | 15 +++++++++++++-- config/h3n2/auspice_config.json | 15 +++++++++++++-- config/h3n2/ha/auspice_config.json | 15 +++++++++++++-- config/h3n2/na/auspice_config.json | 15 +++++++++++++-- config/vic/auspice_config.json | 15 +++++++++++++-- config/vic/ha/auspice_config.json | 15 +++++++++++++-- config/vic/na/auspice_config.json | 15 +++++++++++++-- profiles/ci/builds.yaml | 1 + 10 files changed, 118 insertions(+), 18 deletions(-) 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