feat: add CY114383 to seasonal-flu/nextclade pipeline

nextclade/config/config_dict.yaml

@@ -88,6 +88,12 @@ builds:
           hardmin_date: 2004
           reference_EPI_ISL: EPI1857215
           reference_strain: A/Darwin/6/2021
+        CY114383:
+          filter: "--min-date 2009 --probabilistic-sampling --group-by year region --min-length 1400 --subsample-max-sequences 1500"
+          clade_offset: 0
+          hardmin_date: 2004
+          reference_EPI_ISL: EPI115646
+          reference_strain: A/Wisconsin/67/2005
   vic:
     ha:
       changelog: "seasonal_B-Vic_HA/main/CHANGELOG.md"

nextclade/dataset_config/h3n2/na/CY114383/README.md

@@ -0,0 +1,35 @@
+# Influenza A(H3N2) NA based on reference "A/Wisconsin/67/2005"
+
+| Key                  | Value                |
+| -------------------- | -------------------- |
+| authors                | [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org)                         |
+| name                 | Influenza A H3N2 NA                      |
+| reference            | A/Wisconsin/67/2005                     |
+| dataset path         | flu/h3n2/na/CY114383                     |
+| reference accession  | EPI115646   |
+| clade definitions  |  [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_NA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_NA/)  |
+
+
+
+## Features
+This dataset supports
+
+ * Assignment to clades and subclades based on the nomenclature defined in [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_NA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_NA/)
+ * Identification of glycosilation motifs
+ * Counting of mutations in the RBD
+ * Sequence QC
+ * Phylogenetic placement
+
+## Clades of seasonal influenza viruses
+
+The WHO Collaborating centers **do not** define "clades" for the neuraminidase segment.
+
+This dataset focuses on "subclades" that in analogy to the HA segment are defined to break down diversity at high resolution and allow following the spread of different viral groups.
+These follow a Pango-like nomenclature consisting of a letter followed by a numbers separated by periods as in `C.1.2`.
+The leading letter is an alias of a previous name.
+Details of the nomenclature system can be found at [github.com/influenza-clade-nomenclature/seasonal_A-H3N2_NA/](https://github.com/influenza-clade-nomenclature/seasonal_A-H3N2_NA/).
+
+
+## What is Nextclade dataset
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

nextclade/dataset_config/h3n2/na/CY114383/annotation.gff

@@ -0,0 +1,3 @@
+##gff-version 3
+##sequence-region CY114383 1 1436
+CY114383	feature	gene	4	1413	.	+	.	gene_name="NA"

nextclade/dataset_config/h3n2/na/CY114383/pathogen.json

@@ -0,0 +1,26 @@
+{
+    "nucMutLabelMap": {},
+    "nucMutLabelMapReverse": {},
+    "shortcuts": [
+      "flu_h3n2_na_broad",
+      "nextstrain/flu/h3n2/na",
+      "nextstrain/flu/h3n2/na/wisconsin-67-2005"
+    ],
+      "aaMotifs": [
+      {
+        "name": "glycosylation",
+        "nameShort": "Glyc.",
+        "nameFriendly": "Glycosylation",
+        "description": "N-linked glycosylation motifs (N-X-S/T with X any amino acid other than P)",
+        "includeCdses": [
+          {
+            "cds":"NA",
+            "ranges":[{"begin":29, "end":466}]
+          }
+        ],
+        "motifs": [
+          "N[^P][ST]"
+        ]
+      }
+    ]
+}

nextclade/dataset_config/h3n2/na/CY114383/reference.fasta

@@ -0,0 +1,22 @@
+>CY114383
+AAGATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATATGCTTCT
+TCATGCAAATTGCCATCTTGATAACTACTGTAACATTGCATTTCAAGCAATATGAATTCAACTCCCCCCC
+AAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGAAACATAACAGAGATAGTGTATCTGACC
+AACACCACCATAGAGAAGGAAATATGCCCCAAACTAGCAGAATACAGAAATTGGTCAAAGCCGCAATGTA
+ACATTACAGGATTTGCACCTTTTTCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGT
+GACAAGAGAACCTTATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGGCAGGGAACAACA
+CTAAACAACGTGCATTCAAATGACACAGTACATGATAGGACCCCTTATCGGACCCTATTGATGAATGAGT
+TAGGTGTTCCATTTCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGCTCAAGTTGTCACGATGG
+AAAAGCATGGCTGCATGTTTGTGTAACGGGGGATGATAAAAATGCAACTGCTAGCTTCATTTACAATGGG
+AGGCTTGTAGATAGTATTGTTTCATGGTCCAAAGAAATCCTCAGGACCCAGGAGTCAGAATGCGTTTGTA
+TCAATGGAACTTGTACAGTAGTAATGACTGATGGGAGTGCTTCAGGAAAAGCTGATACTAAAATACTATT
+CATTGAGGAGGGGAAAATCGTTCATACTAGCACATTGTCAGGAAGTGCTCAGCATGTCGAGGAGTGCTCC
+TGCTATCCTCGATATCTTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGCTCCAATAGGCCCATAG
+TAGATATAAACATAAAGGATTATAGCATTGTTTCCAGTTATGTGTGCTCAGGACTTGTTGGAGACACACC
+CAGAAAAAACGACAGCTCCAGCAGTAGCCATTGCTTGGATCCTAACAATGAAGAAGGTGGTCATGGAGTG
+AAAGGCTGGGCCTTTGATGATGGAAATGACGTGTGGATGGGAAGAACGATCAGCGAGAAGTTACGCTCAG
+GATATGAAACCTTCAAAGTCATTGAAGGCTGGTCCAACCCTAATTCCAAATTGCAGATAAATAGGCAAGT
+CATAGTTGACAGAGGTAATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAAT
+CGGTGCTTTTATGTGGAGTTGATAAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCAAACAGTA
+TTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGATGGGGCGGACATCAATCT
+CATGCCTATATAAGCTTTCGCAATTTTAGAAAAAAC