Merge pull request #38 from nextstrain/update-readmes-18

Update readmes 18

Author: genehack

ingest/README.md

@@ -1,8 +1,8 @@
-# Ingest workflow
+# Ingest workflow for rubella virus
 
 This workflow ingests public data from NCBI and outputs curated
-metadata and sequences that can be used as input for the phylogenetic
-workflow.
+metadata and sequences that can be used as input for the rubella
+`nextclade` and `phylogenetic` workflows.
 
 If you have another data source or private data that needs to be
 formatted for the phylogenetic workflow, then you can use a similar

ingest/defaults/override_annotations.tsv

@@ -3,4 +3,3 @@ AB047330	1a(WHO)	1a(WHO)
 AF188704	1a(WHO)	1a(WHO)
 JF727653	1a(WHO)	1a(WHO)
 M30776	1a(WHO)	1a(WHO)
-

nextclade/README.md

@@ -1,14 +1,16 @@
 # Rubella Virus Nextclade Dataset Tree
 
 This workflow creates a phylogenetic tree that can be used as part of
-a Nextclade dataset to assign clades to rubella virus samples based on
-[Rubella virus nomenclature update: 2013][].
+a Nextclade dataset to assign genotypes to rubella virus samples based
+on ["Rubella virus nomenclature update: 2013"][].
 
 * Build a tree using samples from the `ingest` output, with the following
   sampling criteria:
   * Force-include the following samples:
-    * genotype reference strains from Table 1 of [Rubella virus
-      nomenclature update: 2013][]
+    * genotype reference strains from Table 1 of ["Rubella virus
+      nomenclature update: 2013"][]
+    * three additional vaccine-derived strains of genotype 1a that
+      were empirically identified during construction of this dataset
 * Assign genotypes to each sample and internal nodes of the tree with
   `augur clades`, using clade-defining mutations in `defaults/clades.tsv`
 * Provide the following coloring options on the tree:
@@ -25,4 +27,4 @@ a Nextclade dataset to assign clades to rubella virus samples based on
   changes to `defaults/clades.tsv` and re-run the workflow
 * Repeat as needed
 
-[Rubella virus nomenclature update: 2013]: https://www.who.int/publications/i/item/WER8832
+["Rubella virus nomenclature update: 2013"]: https://www.who.int/publications/i/item/WER8832

phylogenetic/README.md

@@ -1,7 +1,8 @@
-# Phylogenetic workflow
+# Phylogenetic workflow for rubella virus
 
-This workflow uses metadata and sequences to produce one or multiple
-[Nextstrain datasets][] that can be visualized in Auspice.
+This workflow uses metadata and sequences to produce two
+[Nextstrain datasets][] that can be visualized in Auspice, one for the
+whole rubella genome, and one specific for the E1 gene.
 
 ## Data Requirements