Fix orov dataset based on PR review comments.

- Fix typo: "Oropouch" → "Oropouche" in CHANGELOG.md files
- Fix casing: "oroV" → "OROV" in README.md titles
- Update meta URLs from dezordi/nextclade_data_workflows to
  InstitutoTodosPelaSaude/nextclade-datasets-workflows
- Adjust placementMaskRanges to use 0-based coordinates (off-by-one fix)
- Increase privateMutations cutoff thresholds:
  - L segments: 20 → 30
  - M segments: 15 → 20
  - S segments: 15 → 20
- Add "alignmentPreset": "high-diversity" to L/refseq alignment params
- Add note on truncated 3' UTR to S/refseq README with recommendation
  to use S/tefe for full-length sequences
- Improve tefe CHANGELOG descriptions (e.g. "NCBI tefe" → "Tefe outbreak reference genome")
- Add missing newlines at end of files
- Update tree.json files with refreshed phylogenetic trees

Author: dezordi

data/community/itps/orov/L/refseq/CHANGELOG.md

@@ -1,5 +1,5 @@
 ## Unreleased
 
-Initial release of a Oropouch Virus (OROV) dataset for segment L based on NCBI refseq reference genome.
+Initial release of a Oropouche Virus (OROV) dataset for segment L based on NCBI refseq reference genome.
 
-Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
+Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data/community/itps/orov/L/refseq/README.md

@@ -1,4 +1,4 @@
-# Nextclade Dataset for "oroV" L segment based on RefSeq reference genome
+# Nextclade Dataset for "OROV" L segment based on RefSeq reference genome
 
 ## Dataset Attributes
 
@@ -10,11 +10,11 @@
 
 ## Scope of This Dataset
 
-The dataset aims to enable the quality control of segment L of Oropouche virus using ncbi refseq as reference.
+The dataset aims to enable the quality control of segment L ofOropouche virus using ncbi refseq as reference.
 
 
 The source code is available at [InstitutoTodosPelaSaude/nextclade-datasets-workflows](https://github.com/InstitutoTodosPelaSaude/nextclade-datasets-workflows/tree/main/orov).
 
 For bugs, please open an [issue](https://github.com/InstitutoTodosPelaSaude/nextclade-datasets-workflows/issues).
 
-Read more about Nextclade datasets in the Nextclade documentation: [Nextclade Datasets](https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html).
+Read more about Nextclade datasets in the Nextclade documentation: [Nextclade Datasets](https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html).

data/community/itps/orov/L/refseq/pathogen.json

@@ -1,7 +1,8 @@
 {
   "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json",
   "alignmentParams": {
-    "retryReverseComplement": true
+    "retryReverseComplement": true,
+    "alignmentPreset": "high-diversity"
   },
   "attributes": {
     "name": "orov/L/refseq",
@@ -15,10 +16,10 @@
   "placementMaskRanges": [
     {
       "begin": 0,
-      "end": 44
+      "end": 43
     },
     {
-      "begin": 6797,
+      "begin": 6796,
       "end": 6846
     }
   ],
@@ -35,8 +36,8 @@
     "treeJson": "tree.json"
   },
   "meta": {
-    "bugs": "https://github.com/dezordi/nextclade_data_workflows/issues",
-    "source code": "https://github.com/dezordi/nextclade_data_workflows/tree/main/oroV"
+    "bugs": "https://github.com/InstitutoTodosPelaSaude/nextclade-datasets-workflows/issues",
+    "source code": "https://github.com/InstitutoTodosPelaSaude/nextclade-datasets-workflows/tree/main/orov"
   },
   "qc": {
     "frameShifts": {
@@ -75,7 +76,7 @@
       "mixedSitesThreshold": 7
     },
     "privateMutations": {
-      "cutoff": 20,
+      "cutoff": 30,
       "enabled": true,
       "typical": 10,
       "weightLabeledSubstitutions": 2,
@@ -94,4 +95,4 @@
     "tag": "unreleased"
   },
   "defaultCds": "L"
-}
+}