Merge pull request #192 from nextstrain/export-gisaid-strain-names

Include original GISAID strain name in metadata
nextstrain · Oct 31, 2024 · efaf11b · efaf11b
2 parents b09a501 + 8a59d36
commit efaf11b
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Showing 18 changed files with 51 additions and 127 deletions.
diff --git a/config/h1n1pdm/ha/auspice_config.json b/config/h1n1pdm/ha/auspice_config.json
@@ -210,7 +210,8 @@
   ],
   "display_defaults": {
     "map_triplicate": true,
-    "color_by": "clade_membership"
+    "color_by": "clade_membership",
+    "tip_label": "gisaid_strain"
   },
   "filters": [
     "clade_membership",
@@ -231,6 +232,7 @@
     "frequencies"
   ],
   "metadata_columns": [
+    "gisaid_strain",
     "accession_ha",
     "accession_na"
   ]

diff --git a/config/h1n1pdm/na/auspice_config.json b/config/h1n1pdm/na/auspice_config.json
@@ -175,7 +175,8 @@
   ],
   "display_defaults": {
     "map_triplicate": true,
-    "color_by": "clade_membership"
+    "color_by": "clade_membership",
+    "tip_label": "gisaid_strain"
   },
   "filters": [
     "clade_membership",
@@ -196,6 +197,7 @@
     "frequencies"
   ],
   "metadata_columns": [
+    "gisaid_strain",
     "accession_ha",
     "accession_na"
   ]

diff --git a/config/h3n2/ha/auspice_config.json b/config/h3n2/ha/auspice_config.json
@@ -227,7 +227,8 @@
   ],
   "display_defaults": {
     "map_triplicate": true,
-    "color_by": "clade_membership"
+    "color_by": "clade_membership",
+    "tip_label": "gisaid_strain"
   },
   "filters": [
     "clade_membership",
@@ -248,6 +249,7 @@
     "frequencies"
   ],
   "metadata_columns": [
+    "gisaid_strain",
     "accession_ha",
     "accession_na"
   ]

diff --git a/config/h3n2/na/auspice_config.json b/config/h3n2/na/auspice_config.json
@@ -160,7 +160,8 @@
   ],
   "display_defaults": {
     "map_triplicate": true,
-    "color_by": "clade_membership"
+    "color_by": "clade_membership",
+    "tip_label": "gisaid_strain"
   },
   "filters": [
     "clade_membership",
@@ -181,6 +182,7 @@
     "frequencies"
   ],
   "metadata_columns": [
+    "gisaid_strain",
     "accession_ha",
     "accession_na"
   ]

diff --git a/config/vic/ha/auspice_config.json b/config/vic/ha/auspice_config.json
@@ -167,7 +167,8 @@
   ],
   "display_defaults": {
     "map_triplicate": true,
-    "color_by": "clade_membership"
+    "color_by": "clade_membership",
+    "tip_label": "gisaid_strain"
   },
   "filters": [
     "clade_membership",
@@ -188,6 +189,7 @@
     "frequencies"
   ],
   "metadata_columns": [
+    "gisaid_strain",
     "accession_ha",
     "accession_na"
   ]

diff --git a/config/vic/na/auspice_config.json b/config/vic/na/auspice_config.json
@@ -160,7 +160,8 @@
   ],
   "display_defaults": {
     "map_triplicate": true,
-    "color_by": "clade_membership"
+    "color_by": "clade_membership",
+    "tip_label": "gisaid_strain"
   },
   "filters": [
     "clade_membership",
@@ -181,6 +182,7 @@
     "frequencies"
   ],
   "metadata_columns": [
+    "gisaid_strain",
     "accession_ha",
     "accession_na"
   ]

diff --git a/profiles/nextflu-private-forecasts.yaml b/profiles/nextflu-private-forecasts.yaml
@@ -4,30 +4,6 @@ custom_rules:
   - profiles/nextflu-private-forecasts/zoltar.smk
   - profiles/nextflu-private-forecasts/rename.smk
 
-fasta_fields:
-  - strain
-  - virus
-  - segment
-  - accession
-  - date
-  - date_submitted
-  - region
-  - country
-  - division
-  - location
-  - passage_category
-  - originating_lab
-  - submitting_lab
-  - age
-  - gender
-prettify_fields:
-  - region
-  - country
-  - division
-  - location
-  - originating_lab
-  - submitting_lab
-
 lat-longs: "config/lat_longs.tsv"
 
 segments:

diff --git a/profiles/nextflu-private.yaml b/profiles/nextflu-private.yaml
@@ -7,30 +7,6 @@ custom_rules:
 # URL for auto-deploying builds
 deploy_url: https://nextstrain.org/groups/nextflu-private/
 
-fasta_fields:
-  - strain
-  - virus
-  - segment
-  - accession
-  - date
-  - date_submitted
-  - region
-  - country
-  - division
-  - location
-  - passage_category
-  - originating_lab
-  - submitting_lab
-  - age
-  - gender
-prettify_fields:
-  - region
-  - country
-  - division
-  - location
-  - originating_lab
-  - submitting_lab
-
 lat-longs: "config/lat_longs.tsv"
 
 segments:

diff --git a/profiles/nextflu-private/h1n1pdm/ha/auspice_config.json b/profiles/nextflu-private/h1n1pdm/ha/auspice_config.json
@@ -461,5 +461,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_strain",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/profiles/nextflu-private/h1n1pdm/na/auspice_config.json b/profiles/nextflu-private/h1n1pdm/na/auspice_config.json
@@ -202,5 +202,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_strain",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/profiles/nextflu-private/h3n2/ha/auspice_config.json b/profiles/nextflu-private/h3n2/ha/auspice_config.json
@@ -593,5 +593,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_strain",
+    "accession_ha",
+    "accession_na"
   ]
-}
+}
diff --git a/profiles/nextflu-private/h3n2/na/auspice_config.json b/profiles/nextflu-private/h3n2/na/auspice_config.json
@@ -236,5 +236,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_strain",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/profiles/nextflu-private/vic/ha/auspice_config.json b/profiles/nextflu-private/vic/ha/auspice_config.json
@@ -303,5 +303,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_strain",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/profiles/nextflu-private/vic/na/auspice_config.json b/profiles/nextflu-private/vic/na/auspice_config.json
@@ -180,5 +180,10 @@
     "map",
     "entropy",
     "frequencies"
+  ],
+  "metadata_columns": [
+    "gisaid_strain",
+    "accession_ha",
+    "accession_na"
   ]
 }
diff --git a/profiles/nextstrain-public-yamagata.yaml b/profiles/nextstrain-public-yamagata.yaml
@@ -6,30 +6,6 @@ custom_rules:
 # URL for auto-deploying builds
 deploy_url: s3://nextstrain-data
 
-fasta_fields:
-  - strain
-  - virus
-  - segment
-  - accession
-  - date
-  - date_submitted
-  - region
-  - country
-  - division
-  - location
-  - passage_category
-  - originating_lab
-  - submitting_lab
-  - age
-  - gender
-prettify_fields:
-  - region
-  - country
-  - division
-  - location
-  - originating_lab
-  - submitting_lab
-
 lat-longs: "config/lat_longs.tsv"
 
 segments:

diff --git a/profiles/nextstrain-public.yaml b/profiles/nextstrain-public.yaml
@@ -6,30 +6,6 @@ custom_rules:
 # URL for auto-deploying builds
 deploy_url: s3://nextstrain-data
 
-fasta_fields:
-  - strain
-  - virus
-  - segment
-  - accession
-  - date
-  - date_submitted
-  - region
-  - country
-  - division
-  - location
-  - passage_category
-  - originating_lab
-  - submitting_lab
-  - age
-  - gender
-prettify_fields:
-  - region
-  - country
-  - division
-  - location
-  - originating_lab
-  - submitting_lab
-
 lat-longs: "config/lat_longs.tsv"
 
 segments:

diff --git a/profiles/private.nextflu.org.yaml b/profiles/private.nextflu.org.yaml
@@ -2,30 +2,6 @@ custom_rules:
   - workflow/snakemake_rules/download_from_s3.smk
   - profiles/private.nextflu.org/export.smk
 
-fasta_fields:
-  - strain
-  - virus
-  - segment
-  - accession
-  - date
-  - date_submitted
-  - region
-  - country
-  - division
-  - location
-  - passage_category
-  - originating_lab
-  - submitting_lab
-  - age
-  - gender
-prettify_fields:
-  - region
-  - country
-  - division
-  - location
-  - originating_lab
-  - submitting_lab
-
 lat-longs: "config/lat_longs.tsv"
 
 segments:

diff --git a/profiles/upload.yaml b/profiles/upload.yaml
@@ -21,6 +21,7 @@ fauna_fasta_fields:
   - submitting_lab
   - age
   - gender
+  - gisaid_strain
 fasta_fields:
   - strain
   - virus
@@ -38,6 +39,7 @@ fasta_fields:
   - submitting_lab
   - age
   - gender
+  - gisaid_strain
 prettify_fields:
   - region
   - country