Merge pull request #10 from nextstrain/provenance

Include data provenance field and update footer
nextstrain · Apr 20, 2023 · 6eaa51d · 6eaa51d
2 parents 1a25888 + 86a1005
commit 6eaa51d
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Showing 6 changed files with 26 additions and 2 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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.
Original file line number	Diff line number	Diff line change
		@@ -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.