Merge pull request #240 from nextstrain/new-lineages

Update nextclade workflow for new clades B.1.21, B.1.22, C.1.1
nextstrain · Apr 17, 2024 · ca836a8 · ca836a8
2 parents 2ed785b + 8e53782
commit ca836a8
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Showing 6 changed files with 54 additions and 14 deletions.
diff --git a/nextclade/README.md b/nextclade/README.md
@@ -24,6 +24,7 @@ nextstrain view auspice/
 
 - [ ] Update each `config/{build}/clades.tsv` with new clades
 - [ ] Add new clades to color ordering
+- [ ] Add representative sequences to `resources/include_accessions.txt`
 - [ ] Check that clades look good, exclude problematic sequences as necessary
 
 ### Creating a new dataset version
@@ -33,15 +34,10 @@ nextstrain view auspice/
 - [ ] Create branch there, copy datasets, commit, push, open PR:
 
 ```bash
-cd ../../nextclade_data
-git checkout master
-git pull
-git checkout -b mpox-update
-cp -r ../monkeypox/nextclade/datasets/ data/nextstrain/mpox
-git add data/nextstrain/mpox
-git commit -m "Update mpox dataset"
-git push -u origin mpox-update
-gh pr create
+cd ~/code
+cp mpox/nextclade/datasets/all-clades/tree.json nextclade_data/data/nextstrain/mpox/all-clades/tree.json
+cp mpox/nextclade/datasets/clade-iib/tree.json nextclade_data/data/nextstrain/mpox/clade_iib/tree.json
+p mpox/nextclade/datasets/lineage-b.1/tree.json nextclade_data/data/nextstrain/mpox/lineage-b.1/tree.json
 ```
 
 ## Configuration

diff --git a/nextclade/resources/all-clades/clades.tsv b/nextclade/resources/all-clades/clades.tsv
@@ -63,6 +63,10 @@ C.1	nuc	55133	A
 C.1	nuc	64426	T
 C.1	nuc	105923	A
 
+C.1.1	clade	C.1
+C.1.1	nuc	21062	T
+C.1.1	nuc	149963	T
+
 B.1.4	clade	B.1
 B.1.4	nuc	34308	A
 
@@ -124,4 +128,12 @@ B.1.19	nuc	148268	T
 B.1.20	clade	B.1
 B.1.20	nuc	53326	A
 B.1.20	nuc	164385	T
-B.1.20	nuc	187620	T
+B.1.20	nuc	187620	T
+
+B.1.21	clade	B.1
+B.1.21	nuc	22415	A
+B.1.21	nuc	132698	T
+
+B.1.22	clade	B.1
+B.1.22	nuc	34784	T
+B.1.22	nuc	101418	T
diff --git a/nextclade/resources/clade-iib/clades.tsv b/nextclade/resources/clade-iib/clades.tsv
@@ -64,6 +64,10 @@ C.1	nuc	55133	A
 C.1	nuc	64426	T
 C.1	nuc	105923	A
 
+C.1.1	clade	C.1
+C.1.1	nuc	21062	T
+C.1.1	nuc	149963	T
+
 B.1.4	clade	B.1
 B.1.4	nuc	34308	A
 
@@ -125,4 +129,12 @@ B.1.19	nuc	148268	T
 B.1.20	clade	B.1
 B.1.20	nuc	53326	A
 B.1.20	nuc	164385	T
-B.1.20	nuc	187620	T
+B.1.20	nuc	187620	T
+
+B.1.21	clade	B.1
+B.1.21	nuc	22415	A
+B.1.21	nuc	132698	T
+
+B.1.22	clade	B.1
+B.1.22	nuc	34784	T
+B.1.22	nuc	101418	T
diff --git a/nextclade/resources/color_ordering.tsv b/nextclade/resources/color_ordering.tsv
@@ -236,6 +236,7 @@ lineage	B.1.1
 lineage	B.1.2
 lineage	B.1.3
 lineage	C.1
+lineage	C.1.1
 lineage	B.1.4
 lineage	B.1.5
 lineage	B.1.6
@@ -253,6 +254,8 @@ lineage	B.1.17
 lineage	B.1.18
 lineage	B.1.19
 lineage	B.1.20
+lineage	B.1.21
+lineage	B.1.22
 lineage	A.2
 lineage	A.2.1
 lineage	A.2.2

diff --git a/nextclade/resources/include_accessions.txt b/nextclade/resources/include_accessions.txt
@@ -1,5 +1,4 @@
 ON563414    #prototypical B.1
-LC753968    #reference for C.1
 ON563414    #reference for B.1
 ON843175    #reference for B.1.9
 OP215224    #reference for B.1.8
@@ -15,7 +14,7 @@ ON929079    #reference for B.1.2
 OP442552    #reference for B.1.17
 ON694335    #reference for B.1.15
 OP693647    #reference for B.1.16
-OP642395     #reference for B.1.16
+OP642395    #reference for B.1.16
 ON694342    #reference for B.1.14
 OP838893    #reference for B.1.19
 OP169336    #reference for B.1.11
@@ -26,3 +25,9 @@ OP536663    #reference for B.1.13
 OP257254    #reference for B.1.13
 OP205110    #reference for B.1.10
 OQ320441    #reference for B.1.20
+OP539939    #reference for B.1.21
+OQ773522    #reference for B.1.22
+OR095023    #reference for B.1.22
+LC753968    #reference for C.1
+LC753968    #reference for C.1.1
+OR643705    #reference for C.1.1
diff --git a/nextclade/resources/lineage-b.1/clades.tsv b/nextclade/resources/lineage-b.1/clades.tsv
@@ -24,6 +24,10 @@ C.1	nuc	55133	A
 C.1	nuc	64426	T
 C.1	nuc	105923	A
 
+C.1.1	clade	C.1
+C.1.1	nuc	21062	T
+C.1.1	nuc	149963	T
+
 B.1.4	clade	B.1
 B.1.4	nuc	34308	A
 
@@ -85,4 +89,12 @@ B.1.19	nuc	148268	T
 B.1.20	clade	B.1
 B.1.20	nuc	53326	A
 B.1.20	nuc	164385	T
-B.1.20	nuc	187620	T
+B.1.20	nuc	187620	T
+
+B.1.21	clade	B.1
+B.1.21	nuc	22415	A
+B.1.21	nuc	132698	T
+
+B.1.22	clade	B.1
+B.1.22	nuc	34784	T
+B.1.22	nuc	101418	T