From 86a100533ba2fcf7f03ca52af82b891a3624610c Mon Sep 17 00:00:00 2001
From: Trevor Bedford <trevor@bedford.io>
Date: Wed, 19 Apr 2023 15:18:42 -0700
Subject: [PATCH] Include data provenance field and update footer

---
 Snakefile                       | 7 +++++--
 config/auspice_config_h5n1.json | 5 +++++
 config/auspice_config_h5nx.json | 5 +++++
 config/auspice_config_h7n9.json | 5 +++++
 config/auspice_config_h9n2.json | 5 +++++
 config/description.md           | 1 +
 6 files changed, 26 insertions(+), 2 deletions(-)
 create mode 100644 config/description.md

diff --git a/Snakefile b/Snakefile
index 688d605..118ac80 100644
--- a/Snakefile
+++ b/Snakefile
@@ -14,7 +14,8 @@ rule files:
         colors = "config/colors_{subtype}.tsv",
         lat_longs = "config/lat_longs_{subtype}.tsv",
         auspice_config = "config/auspice_config_{subtype}.json",
-        clades_file = "clade-labeling/{subtype}-clades.tsv"
+        clades_file = "clade-labeling/{subtype}-clades.tsv",
+        description = "config/description.md"
 
 files = rules.files.params
 
@@ -293,7 +294,8 @@ rule export:
         cleavage_site_sequences = rules.cleavage_site.output.cleavage_site_sequences,
         colors = files.colors,
         lat_longs = files.lat_longs,
-        auspice_config = files.auspice_config
+        auspice_config = files.auspice_config,
+        description = files.description
     output:
         auspice_json = "auspice/flu_avian_{subtype}_{segment}.json"
     shell:
@@ -305,6 +307,7 @@ rule export:
             --colors {input.colors} \
             --lat-longs {input.lat_longs} \
             --auspice-config {input.auspice_config} \
+            --description {input.description} \
             --include-root-sequence \
             --output {output.auspice_json}
         """
diff --git a/config/auspice_config_h5n1.json b/config/auspice_config_h5n1.json
index cc3ac29..5fdcebe 100644
--- a/config/auspice_config_h5n1.json
+++ b/config/auspice_config_h5n1.json
@@ -4,6 +4,11 @@
     {"name": "Louise Moncla", "url": "http://bedford.io/team/louise-moncla/"}
   ],
   "build_url": "https://github.com/nextstrain/avian-flu",
+  "data_provenance": [
+    {
+      "name": "GISAID"
+    }
+  ],
   "colorings": [
     {
       "key": "gt",
diff --git a/config/auspice_config_h5nx.json b/config/auspice_config_h5nx.json
index f75b38c..fd6d845 100644
--- a/config/auspice_config_h5nx.json
+++ b/config/auspice_config_h5nx.json
@@ -4,6 +4,11 @@
     {"name": "Louise Moncla", "url": "http://bedford.io/team/louise-moncla/"}
   ],
   "build_url": "https://github.com/nextstrain/avian-flu",
+  "data_provenance": [
+    {
+      "name": "GISAID"
+    }
+  ],  
   "colorings": [
     {
       "key": "gt",
diff --git a/config/auspice_config_h7n9.json b/config/auspice_config_h7n9.json
index 51fbd84..2c43942 100644
--- a/config/auspice_config_h7n9.json
+++ b/config/auspice_config_h7n9.json
@@ -4,6 +4,11 @@
     {"name": "Louise Moncla", "url": "http://bedford.io/team/louise-moncla/"}
   ],
   "build_url": "https://github.com/nextstrain/avian-flu",
+  "data_provenance": [
+    {
+      "name": "GISAID"
+    }
+  ],  
   "colorings": [
     {
       "key": "gt",
diff --git a/config/auspice_config_h9n2.json b/config/auspice_config_h9n2.json
index b16f117..1dc89ea 100644
--- a/config/auspice_config_h9n2.json
+++ b/config/auspice_config_h9n2.json
@@ -4,6 +4,11 @@
     {"name": "Louise Moncla", "url": "http://bedford.io/team/louise-moncla/"}
   ],
   "build_url": "https://github.com/nextstrain/avian-flu",
+  "data_provenance": [
+    {
+      "name": "GISAID"
+    }
+  ],
   "colorings": [
     {
       "key": "gt",
diff --git a/config/description.md b/config/description.md
new file mode 100644
index 0000000..3bf9e7e
--- /dev/null
+++ b/config/description.md
@@ -0,0 +1 @@
+We thank the [GISAID Initiative](https://gisaid.org) and the [GISRS Network](http://www.who.int/influenza/gisrs_laboratory/en/) for critical surveillance efforts and open data sharing. We gratefully acknowledge the authors, originating and submitting laboratories of sequences from the GISAID EpiFlu Database on which this research is based. An attribution table is available by clicking on "Download Data" at the bottom of the page and then clicking on "Acknowledgments" in the resulting dialog box.