Add orov datasets

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

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+## Unreleased
+
+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

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

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+# Nextclade Dataset for "OROV" L segment based on RefSeq reference genome
+
+## Dataset Attributes
+
+| Attribute            | Value                                    |
+| -------------------- | ---------------------------------------- |
+| Name                 | orov/L/refseq                            |
+| RefName              | Oropouche virus segment L                |
+| RefAccession         | NC_005776.1                              |
+
+## Scope of This Dataset
+
+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).

data/community/itps/orov/L/refseq/genome_annotation.gff3

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+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+##sequence-region NC_005776.1 1 6846
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118655
+NC_005776.1	RefSeq	region	1	6846	.	+	.	ID=NC_005776.1:1..6846;Dbxref=taxon:118655;Name=L;gbkey=Src;genome=genomic;mol_type=genomic RNA;segment=L
+NC_005776.1	GenBank	gene	44	6796	.	+	.	gene_name=L

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

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+{
+  "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json",
+  "alignmentParams": {
+    "retryReverseComplement": true,
+    "alignmentPreset": "high-diversity"
+  },
+  "attributes": {
+    "name": "orov/L/refseq",
+    "reference accession": "NC_005776.1",
+    "reference name": "Oropouche virus, L segment"
+  },
+  "compatibility": {
+    "cli": "3.0.0-alpha.0",
+    "web": "3.0.0-alpha.0"
+  },
+  "placementMaskRanges": [
+    {
+      "begin": 0,
+      "end": 43
+    },
+    {
+      "begin": 6796,
+      "end": 6846
+    }
+  ],
+  "deprecated": false,
+  "enabled": true,
+  "experimental": true,
+  "files": {
+    "changelog": "CHANGELOG.md",
+    "examples": "sequences.fasta",
+    "genomeAnnotation": "genome_annotation.gff3",
+    "pathogenJson": "pathogen.json",
+    "readme": "README.md",
+    "reference": "reference.fasta",
+    "treeJson": "tree.json"
+  },
+  "meta": {
+    "bugs": "https://github.com/InstitutoTodosPelaSaude/nextclade-datasets-workflows/issues",
+    "source code": "https://github.com/InstitutoTodosPelaSaude/nextclade-datasets-workflows/tree/main/orov"
+  },
+  "qc": {
+    "frameShifts": {
+      "enabled": true,
+      "ignoredFrameShifts": [
+        {
+          "codonRange": {
+            "begin": 788,
+            "end": 792
+          },
+          "cdsName": "L"
+        },
+        {
+          "codonRange": {
+            "begin": 797,
+            "end": 800
+          },
+          "cdsName": "L"
+        },
+        {
+          "codonRange": {
+            "begin": 846,
+            "end": 855
+          },
+          "cdsName": "L"
+        }
+      ]
+    },
+    "missingData": {
+      "enabled": true,
+      "missingDataThreshold": 1369,
+      "scoreBias": 95
+    },
+    "mixedSites": {
+      "enabled": true,
+      "mixedSitesThreshold": 7
+    },
+    "privateMutations": {
+      "cutoff": 30,
+      "enabled": true,
+      "typical": 10,
+      "weightLabeledSubstitutions": 2,
+      "weightReversionSubstitutions": 1,
+      "weightUnlabeledSubstitutions": 1
+    },
+    "snpClusters": {
+      "enabled": false
+    },
+    "stopCodons": {
+      "enabled": true
+    }
+  },
+  "schemaVersion": "3.0.0",
+  "version": {
+    "tag": "unreleased"
+  },
+  "defaultCds": "L"
+}

data/community/itps/orov/L/refseq/reference.fasta

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+>NC_005776.1 Oropouche virus segment L, complete genome
+AGTAGTGTGCTCCTATTCCGAAACAAACAAAAACAATCTCAAAATGTCACAACTGTTGCT
+CAACCAATATCGGAATAGGATATTGCACTGCCGTGAACCTGAGATAGCAAAGGATATATG
+GCGAGATCTATTAAATGATCGACACAATTACTTTTCTCGGGAATTTTGCAGAGCTGCAAA
+TCTTGAGTACAGAAATGATGTTCCTGCTGAGGATATTTGTGCTGAAGTTCTTGATGGTTA
+TAAAGCAAGGAAAGTTCGCTTTTGTACACCTGATAATTACTTACTACATGATGGAAAGAT
+GTATATAATAGACTTCAAAGTGTCTGTAGACGACCGATCTTCTAGAATCACAAGGGAGAA
+ATATAATGAGATTTTTGGAGAGGTATTCAATCCAGAAGGTGTAGATTTTGAAATTGTTAT
+TATTAGATTAGATCCTTCAAATATGACGATACATGTGGACTCTCGAGATTTCGTGAATAC
+AATTGGGCCGATTACATTAAACATTAGTATGCAATGGTTTTTTGATATGAAAGACTTCTT
+GTTCGGGAAATTTCGGGATGATGATAAATTCCATGCTATAATAAGTCAAGGAGAATTCAC
+AATGACATTGCCATGGATTGAAGAAGACACCCCAGAATTGCTTACTCATCCTATATACAA
+TGAATTCATGAGTTCAATGCCAGAGGCAGAACAGGCCCTATTCAAGGAAGCATTGGAATT
+CAAATCATTTGGGGCAGAAAAATGGAATATCTTTTTGAAGGGGGTGATGTCAAAGTATGG
+TGAATATTATAAAGAATTTACTAAAGGACATGCTCATTCTATATTTCTGACAACAGGGGA
+CTACCCCAAGCCAGACAAAGACCAAATTTCAGCAGGTTGGAGAGAAATGGTAAACAGAGT
+AAGCTCTGAACGTGACATGTCAAATGACATAAATCAGGAAAAACCAAGCATGCATTTTAT
+ATGGGCAAAGAATGATTCAAATAGCAACAATAATATACAAAAGCTAATCAAACTATCTAA
+ATCACTGCAAGCTATGAGCGGGACAGGGAGCTATGTAAATGCTTTCAAGTCATTAGGGAG
+ATTAATGGATATATCATCAGATGTTAAAAAATATGAATCATTTTGTGGGAAATTGAAATC
+TCTGGCAAGGTCTAGTATAAAAAAACTTGACAGGAAAATAGAGCCAATACAAATTGGGAC
+TGCAACTGTCTTATGGGAACAGCAATTTAAACTAGATACAGATGTTATAAAAAGAGAAGA
+CAGAATACATTTAATGAAAGATTATCTTGGGATCGGTAAGCACAAATCATTTTCAAAGAA
+ATTAAACAACGACATAAATACTGATAAGCCTAAAATATTAAATTTCAACAATGATGATAT
+AGTCAGGAAATGCAAAGATAAATATAATCAAGTCATACATAACCTATCCCAAATCAATGA
+ATTAGATAAGATTGGAAACTACCTAGAGCACTTTTCAGCTAAAATTAGTGCCTGCAGTGT
+AGAAATGTGGGATTTTATATATAATACAACCAAAACTAAATACTGGCAATGCATCAATGA
+CTATTCCACCCTAATGAAAAACATGTTAGCTGTCTCTCAATATAATAGACACAATACGTT
+TAGAATTGTCTCATGTGCAAACAATAATGTATTTGGTCTAGTAATGCCAAGCTCAGATAT
+AAAGACAAAAAAAGCAACTTTAGTCTATGCAATAATGGCTCTCCATAATGAGGAGGCAGA
+AATAGCAGAACTTGGCTCACTCTACTCAACTTTTAAGACAGCAACAGGATATATTTCAAT
+ATCAAAGGCTTTTAGGCTGGATAAAGAAAGATGCCAACGCATAGTATCCTCTCCAGGCTT
+GTTCCTCATGACAAGCTGCCTATTATTCAACGGTAACAAGAGTTTAGAATTTGATAAATT
+ACTAGGATTTTCATTTTTTACGTCAATATCAATTACGAAAGCTATGCTCTCCCTTACTGA
+GCCTTCACGTTATATGATCATGAACTCGTTAGCAGTTTCCAGCCATGTAAGAGAGTATAT
+ATCTGAAAAATTCTCCCCTTATACAAAAACATCATTTTCTGTGGTAATGACAGACTTAAT
+CAAGAAGGGTTGCTATTCAGCATATGAACAGAGAAAAAAAGTACAAATAAGAGACATAAA
+ATTAACAGATTATGATATAACACAAAAGGGAGTGGATTCCAAAAGAGATCTTAAATCTAT
+TTGGTTCCCAGGAAAGGTAAACCTGAAAGAATATTTAAACCAAATTTATCTACCATTTTA
+TTTTAACTCTAAAGGATTACATGAAAAACATCATGTCTTGATAGATTTGGCTAAAACAGT
+ACTAGAAATCGAAAAAGAGCAAAGGGAGTCATTACCTGAGCCATGGTCAGAGATACCTGC
+TAAGCGACTGTCACTTAATGTTTTAATTTACTCATTGCAGGAACTGAATTTAGATACTTC
+AAGACATAATTTTGTAAGAAGCCGGGTGGAAAACGCAAATAATTTCAACAGATCTATAAC
+GACAATATCTACTTTTACCAGCTCAAAATCATGCATTAAGATTGGTGATTTTGAAGAAGA
+AAAAAGAGAAAAACTAAGAATGATACAAAAGAAACTTGCAAAGGATATTTCTAAATTAAC
+CATAGCCAACCCAGCATTCTTAGATGAGATCACAAACGAACATGAGATAAGGCATTCAAC
+TTATGAGGACTTAAAACAATCTATCCCAGATTACACAGATTATATGTCTGTGAAAGTTTT
+TGACAGATTGTACGAGAAGATTACTACCAATGAAATAAATGATAAGGAAACAGTCAAGCT
+GATTCTAGAGACCATGAAAAAACATAAAATATTTCATTTTGGATTCTTCAATAAAGGACA
+AAAAACAGCCAAAGATAGAGAAATATTTTTAGGTGAATTTGAAGCAAAAATGTGTCTGTA
+CCTTGTCGAAAGAATAGCTAAAGAGAGGTGCAAATTAAACCCTGAAGAAATGATAAGTGA
+ACCAGGCGACTCGAAACTAAGGGTATTAGAGAAGCAATCAGAAGACGAAATCAGGTATAT
+TAGCAATACAATAAAGACATTAGGGAATGCCATAGAGAACTTGCAATCTGGATCTTTAAA
+TTGGGCAGATATATGCGAAAACAAAGCAAGAGGACTTAAGATAGAAATAAATGCTGATAT
+GTCCAAATGGAGTGCCCAAGATGTACTTTTTAAATATTTTTGGTTGATAGTGCTTGATCC
+CATCTTATATCCTGCTGAGAGGAAAAGGATAATTTATTTCCTCTGTAATTATATGCAGAA
+AAGGCTTATAATGCCCGATGAATTGCTCACTACTATATTGGATCAAAGAGTTCCTTATTC
+AAATGACATAATTGGATTAATGACAAACAATTATAGGTCTAATACAGTAGAAATAAAGCG
+TAACTGGCTTCAAGGCAACTTAAATTATACAAGCAGTTACTTACACAGCTGTAGTATGTC
+TGTGTACAAAGATATAATAAGAGAAGCAGCAATATTATTAGAAGGAGAAGCCCTTGTGAA
+CTCAATGGTACATTCTGATGATAATCAAACATCTATATGTATGGTGCAGAATAAATTACC
+AGATGACAATATAATTGAATTTTGCATTAAGATATTCGAGAAGATATGCTTAACTTTTGG
+CAATCAGGCAAATATGAAGAAGACATATCTAACTAACTTCATCAAAGAGTTTGTTTCTTT
+ATTTAATATACATGGAGAACCATTTTCTATATATGGGAGATTTCTACTCACAGCAGTAGG
+AGACTGTGCCTATCTAGGGCCTTATGAAGATTTAGCAAGTAGGCTATCTGCAACACAAAC
+TGCTATAAAGCATGGTTGCCCACCATCACTTGCATGGGTATCTATCGCTCTAAATCACTG
+GATAACCCACACTACATATAATATGTTGCCTGGCCAAAATAATGACCCGTTACCATTCTT
+CCCTACTAACAATAGAAGTGAAATACCAGTAGAGATGTGCGGAATACTAGAAAGTGATTT
+ATCAACAATTGCACTAACTGGTTTAGAAGCAGGGAATGTCACGTTTCTAACAAATATAGC
+AAGGAAGTTATCATCCCCAATCTTACAAAGAGAAAGTATTCAAGATCAATACAATTCTAT
+AGAAAAGTGGGATCTGAGCAAATTATCACAGATCGACATTCTAAGGCTTAAAATGCTCAG
+GTATATATCTCTTGATAGTTCAGTCACATCTGATGATGGTATGGGGGAGACTAGTGAAAT
+GAGATCTCGATCACTTTTAACACCTCGTAAATTCACAACAAGTGGGTCACTTAATAGGTT
+GAAATCATATAAAGACTTTCAAGATATAATAGCAGATGAGGACAAGACAAACGAACTATT
+TGAGAATTTCATTAGACACCCAGAGTTACTGGTTACAAAAGGCGAAACATTTGAAGAATT
+TGTTAATACGATATTATTTAGGTACAATTCAAAGAAATTCAAAGAATCTTTGTCAATACA
+AAACCCAGCACAGCTTTTTATTGAGCAAATATTATTTTCCAATAAACCAGTAATTGACTA
+CACTAGCATACATGACAAGATTTTTGGATTACAAGACATGCCAGGAATTGAAGAACTAGA
+TACAATTATAGGTCGCAAAACATTTGTTGAGAGTTATGTTCAAATCGTAGATGACTTAAG
+CAATTTAACATTGGATATAAACGATGTCAAGACTATATTTGCCTTTTGTCTTATGAATGA
+CCCACTACTGATCACATCTGCTAACAATATAATAATGTCTGTTAAGGGACATAGTCAAGA
+AAGAATAGGTCAATCAGCATGCAAAATGCCAGAGGTCCGAAGTCTAAAACTCATACATTA
+TTCACCAGCAGTTGTTTTGAGAGCCTATGTGAGAGGGCCAACAAATGTACCGAATGTAGA
+TATAGATGAACTTGCAAGGGATCTATCTCATTTAGAAGACTTCATACAAAGTACAAAACT
+CAGAGAAAATATGAGAGAGAGAATAGAAATAAATGAGAAGCGGCACTTAGGAAGGGATTT
+CAAATTTGAAATCAAAGAACTAACTAGATTTTACCAAGTGTGTTATGATTACATAAAGTC
+TACAGAACATAAAGTCAAGGTATTCATATTGCCATACAAAGTTTTCACATCAATAGAATT
+CTGCGGGGCACTGACAGGTAACTTGATAAATGACAAATTATGGTACATAACGCATTATCT
+GAAAAATATAGTGTCTACTACACATAAGGCACAAATTTCTTCTTCACCTGAATTGGAATT
+GCAAATTGCTGATGAGGCACTAAGACTAGTAGCACATTTTGCTGATACTTTCTTGGCATC
+AGAATCAAGAATACAATTTCTGAAGAAAATTATTGAAGAATTCACATACAAAGGGATACC
+TGTAAAACATTTATACTCAAAAATAAAGAACTCCAAGTTGAGGGTTAAATTTCTAGGGAT
+TCTTTTATGGTTAGATGATCTAACACAGAATGATCTGGATAAATTTGATGCAGATAAATC
+AGATGAAAAGATTATATGGAATAACTGGCAAGTGTCAAGAGATATGAATACTGGACCAAT
+AGACTTAATGATAAGCGGTTACTCTAGACAGCTGCGGATCACTGGGGAAGATGACAAATT
+GATTGCTGCTGAATTGCAGGTTACTAGATTGTCAGAAGATTTAATTTATAGACACGGTCA
+GGCAATGTTGAATAAGCCACACGGCTTAAAGCTTGAAAAAATGCAACCTGTGACTGAGAT
+GTCTAAACGATTACATTATATCGTTTTCCAGCAAAGATCACGGAAACGATACTTCTATTC
+TATATTACCCACCCAAGTAATTGAGGACCATAATTCTAGAGTTGAATCATCTAGGCTAAG
+CAGAGATTCAAAATGGGTTCCTGTATGCCCTGTTGCAATATCAAAACTCTACCAACAAGG
+ACGGCCTATACTTTCCAAAGTTAGAAATCTGAATATGCAGACTCATTCGCTTTCCAGAAT
+ACAAGTTAATGTAGATGAATATGCCATCACGAGAAGAGCACATTTTCAGAAAATGCCTTT
+CTTCGAAGGACCATCAATCCCTTCTGGTGGTATGGATTTGTCTGAGTTGATGAAATCTAC
+ATCCCTATTAAGCTTGAATTATGATAACATAAAAAATGCATCCTTATTGGACATGTCTAG
+GGTATTTAAGTGCAATGGCAGTGGAGATGACCAAATGGCTTTCGAATTTCTATCGGACGA
+AATTTTGGAGCAAGATGTAGTTGAAGAAATAGAATGCAACCCTATATTTTCTATTAGTTA
+TACAAAAAGAGGAGAATCCAATATGACTTATAAAAATGCTTTCCACAAAGCCTTAATCTC
+AGAATGTGACAAATTTGAAGAAGCATTTGACTTCCTCGACATGGGATTTTGCTCGAATGA
+AAATCTTAGTATTCTGGAGGAAATACATTGGATAATCAGTTATTTAAAAACAAATCAATG
+GTCTACGGAACTAGACAATTGTATTCACATGTGCATGTACAGGAATGGATATGATGCAGA
+ATATCATAAATTTGATATACCCTCTAAATTCCTCAAAGACCCAATAAACCGAACAATAAA
+TTGGACTGAAGTCATTGAATTTATATTATTAATTGAAGATTTCCAAACAAAAATTGAGCC
+ATGGTCTAGTATGAAGTCACACTTCTGTTCAAAAGCACACAGTGTAGCACTAGAGTGTAT
+GAAAAATGAGAAAAGATCATTGGCAGAATTTGTAGACAAAAGTAAGAAAACTGGCAAATC
+CAAATTTGACTTCTAAGGTATACACATGTAAAAGTAGTGTTTGTTTCTAAATAGGAGCAC
+ACTACT