From ae1c054dc9d2e3111bdc77d9a167f1c4072e3f6b Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Tue, 10 Sep 2024 14:19:00 -0700 Subject: [PATCH 1/3] nextclade: Update workflow to use `gisaid_epi_isl` Following 2e8211dd1b03b57ba92b835826d6a5e18a57cf27, the column `isolate_id` has been renamed to `gisaid_epi_isl`. --- nextclade/Snakefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextclade/Snakefile b/nextclade/Snakefile index f9800ec4..a2aebcc9 100644 --- a/nextclade/Snakefile +++ b/nextclade/Snakefile @@ -410,8 +410,8 @@ rule export: output: auspice_json="build/{lineage}/{segment}/{reference}/auspice.json", params: - fields="strain region country date isolate_id accession_{segment}", - select_fields = ','.join(["strain", "region", "country", "date", "isolate_id", "accession_{segment}"]), + fields="strain region country date gisaid_epi_isl accession_{segment}", + select_fields = ','.join(["strain", "region", "country", "date", "gisaid_epi_isl", "accession_{segment}"]), date=datetime.datetime.utcnow().strftime("%Y-%m-%d"), shell: """ From d5e1e56a5f2ce2a9f8041b361465f62b434592c1 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Tue, 10 Sep 2024 14:23:17 -0700 Subject: [PATCH 2/3] Update Auspice config JSONs to include `gisaid_epi_isl` Including the `gisaid_epi_isl` as a metadata column so it can be included in acknowledgements. --- config/h1n1pdm/auspice_config.json | 3 +++ config/h1n1pdm/ha/auspice_config.json | 3 +++ config/h1n1pdm/na/auspice_config.json | 3 +++ config/h3n2/auspice_config.json | 3 +++ config/h3n2/auspice_config_fitness.json | 3 +++ config/h3n2/ha/auspice_config.json | 3 +++ config/h3n2/na/auspice_config.json | 3 +++ config/vic/auspice_config.json | 3 +++ config/vic/ha/auspice_config.json | 3 +++ config/vic/na/auspice_config.json | 3 +++ config/yam/auspice_config.json | 3 +++ 11 files changed, 33 insertions(+) diff --git a/config/h1n1pdm/auspice_config.json b/config/h1n1pdm/auspice_config.json index e44247e8..6acfc526 100644 --- a/config/h1n1pdm/auspice_config.json +++ b/config/h1n1pdm/auspice_config.json @@ -164,5 +164,8 @@ "map", "entropy", "frequencies" + ], + "metadata_columns": [ + "gisaid_epi_isl" ] } diff --git a/config/h1n1pdm/ha/auspice_config.json b/config/h1n1pdm/ha/auspice_config.json index 40239891..b154704a 100644 --- a/config/h1n1pdm/ha/auspice_config.json +++ b/config/h1n1pdm/ha/auspice_config.json @@ -239,5 +239,8 @@ "map", "entropy", "frequencies" + ], + "metadata_columns": [ + "gisaid_epi_isl" ] } diff --git a/config/h1n1pdm/na/auspice_config.json b/config/h1n1pdm/na/auspice_config.json index f3417541..2c03df56 100644 --- a/config/h1n1pdm/na/auspice_config.json +++ b/config/h1n1pdm/na/auspice_config.json @@ -204,5 +204,8 @@ "map", "entropy", "frequencies" + ], + "metadata_columns": [ + "gisaid_epi_isl" ] } diff --git a/config/h3n2/auspice_config.json b/config/h3n2/auspice_config.json index 26d23fbd..eb6f5675 100644 --- a/config/h3n2/auspice_config.json +++ b/config/h3n2/auspice_config.json @@ -174,5 +174,8 @@ "map", "entropy", "frequencies" + ], + "metadata_columns": [ + "gisaid_epi_isl" ] } diff --git a/config/h3n2/auspice_config_fitness.json b/config/h3n2/auspice_config_fitness.json index 937a2279..e27efc9e 100644 --- a/config/h3n2/auspice_config_fitness.json +++ b/config/h3n2/auspice_config_fitness.json @@ -152,5 +152,8 @@ "map", "entropy", "frequencies" + ], + "metadata_columns": [ + "gisaid_epi_isl" ] } diff --git a/config/h3n2/ha/auspice_config.json b/config/h3n2/ha/auspice_config.json index 1d7a787a..69ff9426 100644 --- a/config/h3n2/ha/auspice_config.json +++ b/config/h3n2/ha/auspice_config.json @@ -217,5 +217,8 @@ "map", "entropy", "frequencies" + ], + "metadata_columns": [ + "gisaid_epi_isl" ] } diff --git a/config/h3n2/na/auspice_config.json b/config/h3n2/na/auspice_config.json index 5cc55ded..89de7f23 100644 --- a/config/h3n2/na/auspice_config.json +++ b/config/h3n2/na/auspice_config.json @@ -189,5 +189,8 @@ "map", "entropy", "frequencies" + ], + "metadata_columns": [ + "gisaid_epi_isl" ] } diff --git a/config/vic/auspice_config.json b/config/vic/auspice_config.json index 5241ae67..68a09de8 100644 --- a/config/vic/auspice_config.json +++ b/config/vic/auspice_config.json @@ -149,5 +149,8 @@ "map", "entropy", "frequencies" + ], + "metadata_columns": [ + "gisaid_epi_isl" ] } diff --git a/config/vic/ha/auspice_config.json b/config/vic/ha/auspice_config.json index e2fccd11..55a54af9 100644 --- a/config/vic/ha/auspice_config.json +++ b/config/vic/ha/auspice_config.json @@ -196,5 +196,8 @@ "map", "entropy", "frequencies" + ], + "metadata_columns": [ + "gisaid_epi_isl" ] } diff --git a/config/vic/na/auspice_config.json b/config/vic/na/auspice_config.json index f877353a..a181574d 100644 --- a/config/vic/na/auspice_config.json +++ b/config/vic/na/auspice_config.json @@ -189,5 +189,8 @@ "map", "entropy", "frequencies" + ], + "metadata_columns": [ + "gisaid_epi_isl" ] } diff --git a/config/yam/auspice_config.json b/config/yam/auspice_config.json index 3fb05af9..999423d4 100644 --- a/config/yam/auspice_config.json +++ b/config/yam/auspice_config.json @@ -127,5 +127,8 @@ "map", "entropy", "frequencies" + ], + "metadata_columns": [ + "gisaid_epi_isl" ] } From 6ddfdba7099ccebea365637e668e66c25806ab01 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Tue, 10 Sep 2024 14:29:59 -0700 Subject: [PATCH 3/3] Move `accession_ha` and `accession_na` to metadata columns Following up on @huddlej's comment Instead of using the accessions as colorings to force their inclusion in the build, just include them as `metadata_columns`. --- config/h1n1pdm/auspice_config.json | 14 +++----------- config/h1n1pdm/ha/auspice_config.json | 14 +++----------- config/h1n1pdm/na/auspice_config.json | 14 +++----------- config/h3n2/auspice_config.json | 14 +++----------- config/h3n2/auspice_config_fitness.json | 4 +++- config/h3n2/ha/auspice_config.json | 14 +++----------- config/h3n2/na/auspice_config.json | 14 +++----------- config/vic/auspice_config.json | 14 +++----------- config/vic/ha/auspice_config.json | 14 +++----------- config/vic/na/auspice_config.json | 14 +++----------- config/yam/auspice_config.json | 14 +++----------- 11 files changed, 33 insertions(+), 111 deletions(-) diff --git a/config/h1n1pdm/auspice_config.json b/config/h1n1pdm/auspice_config.json index 6acfc526..64a2b033 100644 --- a/config/h1n1pdm/auspice_config.json +++ b/config/h1n1pdm/auspice_config.json @@ -87,16 +87,6 @@ "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", @@ -166,6 +156,8 @@ "frequencies" ], "metadata_columns": [ - "gisaid_epi_isl" + "gisaid_epi_isl", + "accession_ha", + "accession_na" ] } diff --git a/config/h1n1pdm/ha/auspice_config.json b/config/h1n1pdm/ha/auspice_config.json index b154704a..405816da 100644 --- a/config/h1n1pdm/ha/auspice_config.json +++ b/config/h1n1pdm/ha/auspice_config.json @@ -162,16 +162,6 @@ "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", @@ -241,6 +231,8 @@ "frequencies" ], "metadata_columns": [ - "gisaid_epi_isl" + "gisaid_epi_isl", + "accession_ha", + "accession_na" ] } diff --git a/config/h1n1pdm/na/auspice_config.json b/config/h1n1pdm/na/auspice_config.json index 2c03df56..562344b1 100644 --- a/config/h1n1pdm/na/auspice_config.json +++ b/config/h1n1pdm/na/auspice_config.json @@ -127,16 +127,6 @@ "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", @@ -206,6 +196,8 @@ "frequencies" ], "metadata_columns": [ - "gisaid_epi_isl" + "gisaid_epi_isl", + "accession_ha", + "accession_na" ] } diff --git a/config/h3n2/auspice_config.json b/config/h3n2/auspice_config.json index eb6f5675..18dda4d8 100644 --- a/config/h3n2/auspice_config.json +++ b/config/h3n2/auspice_config.json @@ -97,16 +97,6 @@ "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", @@ -176,6 +166,8 @@ "frequencies" ], "metadata_columns": [ - "gisaid_epi_isl" + "gisaid_epi_isl", + "accession_ha", + "accession_na" ] } diff --git a/config/h3n2/auspice_config_fitness.json b/config/h3n2/auspice_config_fitness.json index e27efc9e..a9c9793c 100644 --- a/config/h3n2/auspice_config_fitness.json +++ b/config/h3n2/auspice_config_fitness.json @@ -154,6 +154,8 @@ "frequencies" ], "metadata_columns": [ - "gisaid_epi_isl" + "gisaid_epi_isl", + "accession_ha", + "accession_na" ] } diff --git a/config/h3n2/ha/auspice_config.json b/config/h3n2/ha/auspice_config.json index 69ff9426..a1828294 100644 --- a/config/h3n2/ha/auspice_config.json +++ b/config/h3n2/ha/auspice_config.json @@ -140,16 +140,6 @@ "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", @@ -219,6 +209,8 @@ "frequencies" ], "metadata_columns": [ - "gisaid_epi_isl" + "gisaid_epi_isl", + "accession_ha", + "accession_na" ] } diff --git a/config/h3n2/na/auspice_config.json b/config/h3n2/na/auspice_config.json index 89de7f23..c27f605c 100644 --- a/config/h3n2/na/auspice_config.json +++ b/config/h3n2/na/auspice_config.json @@ -112,16 +112,6 @@ "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", @@ -191,6 +181,8 @@ "frequencies" ], "metadata_columns": [ - "gisaid_epi_isl" + "gisaid_epi_isl", + "accession_ha", + "accession_na" ] } diff --git a/config/vic/auspice_config.json b/config/vic/auspice_config.json index 68a09de8..601f4bbd 100644 --- a/config/vic/auspice_config.json +++ b/config/vic/auspice_config.json @@ -72,16 +72,6 @@ "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", @@ -151,6 +141,8 @@ "frequencies" ], "metadata_columns": [ - "gisaid_epi_isl" + "gisaid_epi_isl", + "accession_ha", + "accession_na" ] } diff --git a/config/vic/ha/auspice_config.json b/config/vic/ha/auspice_config.json index 55a54af9..4dd55ace 100644 --- a/config/vic/ha/auspice_config.json +++ b/config/vic/ha/auspice_config.json @@ -119,16 +119,6 @@ "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", @@ -198,6 +188,8 @@ "frequencies" ], "metadata_columns": [ - "gisaid_epi_isl" + "gisaid_epi_isl", + "accession_ha", + "accession_na" ] } diff --git a/config/vic/na/auspice_config.json b/config/vic/na/auspice_config.json index a181574d..d925076b 100644 --- a/config/vic/na/auspice_config.json +++ b/config/vic/na/auspice_config.json @@ -112,16 +112,6 @@ "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", @@ -191,6 +181,8 @@ "frequencies" ], "metadata_columns": [ - "gisaid_epi_isl" + "gisaid_epi_isl", + "accession_ha", + "accession_na" ] } diff --git a/config/yam/auspice_config.json b/config/yam/auspice_config.json index 999423d4..41439858 100644 --- a/config/yam/auspice_config.json +++ b/config/yam/auspice_config.json @@ -67,16 +67,6 @@ "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", @@ -129,6 +119,8 @@ "frequencies" ], "metadata_columns": [ - "gisaid_epi_isl" + "gisaid_epi_isl", + "accession_ha", + "accession_na" ] }