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Merge branch 'feat/multiref' into fix/cva16-build-files
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‎.github/workflows/build-and-deploy.yml‎

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on:
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push:
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branches:
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- master
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- staging
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- release
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pull_request:
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repository_dispatch:
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types: build-and-deploy
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workflow_dispatch:
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workflow_call:
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concurrency:
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group: cli-${{ github.workflow }}-${{ github.ref_type }}-${{ github.event.pull_request.number || github.ref || github.run_id }}
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group: cli-${{ github.workflow }}-${{ github.ref_type }}-${{ github.head_ref || github.ref_name || github.run_id }}
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cancel-in-progress: true
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defaults:

‎.github/workflows/validate-pr.yml‎

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name: "validate-pr"
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on:
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pull_request:
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permissions:
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contents: "read"
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concurrency:
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group: "validate-pr-${{ github.event.pull_request.number || github.run_id }}"
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cancel-in-progress: true
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defaults:
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run:
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shell: "bash -euxo pipefail {0}"
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env:
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PYTHONUNBUFFERED: "1"
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jobs:
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validate:
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runs-on: "ubuntu-24.04"
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steps:
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- name: "Checkout PR code"
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uses: "actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683" # v4.2.2
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with:
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repository: "${{ github.event.pull_request.head.repo.full_name }}"
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ref: "${{ github.event.pull_request.head.ref }}"
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fetch-depth: 0
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fetch-tags: true
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- name: "Install system dependencies"
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run: "sudo apt-get install genometools python3 --yes -qq >/dev/null"
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- name: "Install Python dependencies"
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run: "pip3 install -r requirements.txt"
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- name: "Validate GFF files"
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run: "./scripts/validate-gff 'data/'"
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- name: "Rebuild (validation only)"
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id: "rebuild"
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continue-on-error: true
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run: "./scripts/rebuild --input-dir 'data/' --output-dir 'data_output/' --no-pull --allow-dirty"
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- name: "Upload validation artifacts"
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if: "always()"
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uses: "actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02" # v4.6.2
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with:
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name: "validation-output"
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path: "data_output/"
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- name: "Fail if rebuild or validation found errors"
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if: "steps.rebuild.outcome == 'failure'"
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run: "exit 1"

‎data/community/collection.json‎

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"community/pathoplexus/cchfv/M",
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"community/v-gen-lab/chikV/genotypes",
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"community/masphl-bioinformatics/hav/vp1-2b-junction",
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"community/masphl-bioinformatics/hav/whole-genome"
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"community/masphl-bioinformatics/hav/whole-genome",
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"community/itps/zikav"
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]
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}

‎data/community/isuvdl/mazeller/prrsv1/orf5/yimim2025/CHANGELOG.md‎

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## Unreleased
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- Remove invalid `qc.missingData.scoreWeight` and `qc.mixedSites.scoreWeight`
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## 2025-09-09T12:13:13Z
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Add schema definition url to `pathogen.json`. This is a purely technical change, for convenience of dataset authors. The data itself is not modified.

‎data/community/isuvdl/mazeller/prrsv1/orf5/yimim2025/pathogen.json‎

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"missingData": {
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"enabled": true,
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"missingDataThreshold": 2000,
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"scoreBias": 500,
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"scoreWeight": 50
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"scoreBias": 500
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},
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"snpClusters": {
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"enabled": true,
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},
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"mixedSites": {
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"enabled": true,
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"mixedSitesThreshold": 15,
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"scoreWeight": 80
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"mixedSitesThreshold": 15
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},
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"frameShifts": {
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"enabled": true,

‎data/community/isuvdl/mazeller/prrsv2/orf5/yimim2023/CHANGELOG.md‎

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## Unreleased
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- Unify attributes per schema update
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## 2025-09-09T12:13:13Z
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Add schema definition url to `pathogen.json`. This is a purely technical change, for convenience of dataset authors. The data itself is not modified.

‎data/community/isuvdl/mazeller/prrsv2/orf5/yimim2023/pathogen.json‎

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"attributes": {
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"name": "PRRSV-2 ORF5 Lineages, Yim-im & Zhang 2023 Microbiol Spectr",
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"reference accession": "DQ478308.1",
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"reference name": "PRRSV0004437"
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"reference name": "PRRSV0004437",
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"experimental": true
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},
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"compatibility": {
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"cli": "3.0.0-alpha.0",
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"web": "3.0.0-alpha.0"
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},
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"deprecated": false,
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"enabled": true,
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"experimental": true,
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"files": {
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"changelog": "CHANGELOG.md",
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"examples": "sequences.fasta",

‎data/community/itps/zikav/CHANGELOG.md‎

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## Unreleased
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- Move `placementMaskRanges` to tree.json
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- Unify attributes per schema update
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## 2026-03-04T12:40:26Z
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Initial release of a Zika Virus (zikav) dataset for genotype classification!
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Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.htmls

‎data/community/itps/zikav/README.md‎

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# Nextclade Dataset for Zika virus Based on Reference "Natal RGN"
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## Dataset Attributes
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| Attribute | Value |
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| -------------------- | ---------------------------------------- |
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| Name | Zika virus |
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| RefName | Natal RGN |
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| RefAccession | NC_035889.1 |
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## Scope of This Dataset
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The dataset aims to enable rapid and accurate identification of the two main Zika virus genotypes, improving the resolution and speed of phylogenetic classification in routine surveillance networks.
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The source code is available at [InstitutoTodosPelaSaude/nextclade-datasets-workflows](https://github.com/InstitutoTodosPelaSaude/nextclade-datasets-workflows/tree/main/zikav).
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For bugs, please open an [issue](https://github.com/InstitutoTodosPelaSaude/nextclade-datasets-workflows/issues).
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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/zikav/genome_annotation.gff3‎

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##gff-version 3
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#!gff-spec-version 1.21
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#!processor NCBI annotwriter
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##sequence-region NC_035889.1 1 10808
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##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=64320
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NC_035889.1 RefSeq region 1 10808 . + . ID=NC_035889.1:1..10808;Dbxref=taxon:64320;collection-date=2015;country=Brazil: Rio Grande do Norte%2C Natal;gbkey=Src;genome=genomic;isolation-source=fetus' brain autopsy;mol_type=genomic RNA;nat-host=Homo sapiens;strain=Natal RGN
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NC_035889.1 RefSeq region 1 10808 . + . ID=id-NC_035889.1:1..10808;Note=Mature peptides were annotated by RefSeq staff using homoloy to NC_012532.1 and the cleavage sites reported in Kuno and Chang%2C 2007 (PMID 17195954). Questions about the annotation of this sequence should be directed to info@ncbi.nlm.nih.gov.;gbkey=Comment
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NC_035889.1 GenBank CDS 108 473 . + . gene_name=ancC
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NC_035889.1 GenBank CDS 108 419 . + . gene_name=C
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NC_035889.1 GenBank CDS 474 977 . + . gene_name=prM
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NC_035889.1 GenBank CDS 474 752 . + . gene_name=pr
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NC_035889.1 GenBank CDS 753 977 . + . gene_name=M
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NC_035889.1 GenBank CDS 978 2489 . + . gene_name=E
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NC_035889.1 GenBank CDS 2490 3545 . + . gene_name=NS1
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NC_035889.1 GenBank CDS 3546 4223 . + . gene_name=NS2A
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NC_035889.1 GenBank CDS 4224 4613 . + . gene_name=NS2B
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NC_035889.1 GenBank CDS 4614 6464 . + . gene_name=NS3
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NC_035889.1 GenBank CDS 6465 6845 . + . gene_name=NS4A
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NC_035889.1 GenBank CDS 6846 6914 . + . gene_name=2K
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NC_035889.1 GenBank CDS 6915 7667 . + . gene_name=NS4B
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NC_035889.1 GenBank CDS 7668 10376 . + . gene_name=NS5

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