├── .gitattributes ├── .github ├── dependabot.yml └── workflows │ ├── fetch-and-ingest-genbank-master.yml │ ├── fetch-and-ingest-gisaid-master.yml │ ├── shellcheck.yml │ └── update-image.yml ├── .gitignore ├── .shellcheckrc ├── Dockerfile ├── LICENSE ├── README.md ├── Snakefile ├── bin ├── check-annotations ├── check-gisaid-geoRules ├── clean ├── dedup-by-gisaid-id ├── detect-generalizable-geoRules ├── fetch-accession-links ├── fetch-cache-version ├── fetch-from-cog-uk-accessions ├── fetch-from-cog-uk-metadata ├── fetch-from-rki-metadata ├── fetch-from-rki-sequences ├── filter-fasta ├── filter-gisaid-annot-using-transform-log ├── flag-metadata ├── generate-nextclade-version-json ├── gisaid-get-all-clades ├── join-metadata-and-clades ├── join-rows ├── launch-build ├── local-ingest-gisaid ├── merge-open ├── metadata-additions ├── notify-on-additional-info-change ├── notify-on-duplicate-biosample-change ├── notify-on-flagged-metadata-change ├── notify-on-problem-data ├── split-fasta ├── transform-biosample ├── transform-genbank ├── transform-gisaid ├── transform-rki ├── transform-rki-data-to-ndjson ├── transform-to-gisaid-cache └── use-nextclade-cache ├── config ├── debug_sample_genbank.yaml ├── debug_sample_gisaid.yaml ├── genbank.yaml ├── gisaid.yaml ├── local_genbank.yaml └── local_gisaid.yaml ├── data ├── .gitignore ├── genbank │ └── .gitignore └── gisaid │ └── .gitignore ├── defaults └── clade-legacy-mapping.yml ├── docs └── ncbi-virus-all-fields-example.json ├── lib └── utils │ ├── transform.py │ └── transformpipeline │ ├── __init__.py │ ├── _base.py │ ├── datasource.py │ ├── filters.py │ └── transforms.py ├── manual-upload ├── README.md ├── Snakefile └── config.yaml ├── nextstrain-pathogen.yaml ├── requirements.txt ├── scripts └── developer_scripts │ ├── rerun-nextclade-21L.sh │ └── rerun-nextclade.sh ├── source-data ├── accessions.tsv.gz ├── genbank_annotations.tsv ├── gisaid_annotations.tsv ├── gisaid_geoLocationRules.tsv ├── rki_accessions.tsv ├── rki_annotations.tsv └── us-state-codes.tsv ├── vendored ├── .github │ ├── dependabot.yml │ ├── pull_request_template.md │ └── workflows │ │ ├── ci.yaml │ │ └── pre-commit.yaml ├── .gitrepo ├── .pre-commit-config.yaml ├── .shellcheckrc ├── README.md ├── cloudfront-invalidate ├── download-from-s3 ├── fetch-from-ncbi-entrez ├── notify-on-diff ├── notify-on-job-fail ├── notify-on-job-start ├── notify-on-record-change ├── notify-slack ├── s3-object-exists ├── sha256sum ├── trigger ├── trigger-on-new-data └── upload-to-s3 └── workflow └── snakemake_rules ├── curate.smk ├── fetch_sequences.smk ├── nextclade.smk ├── slack_notifications.smk ├── trigger.smk └── upload.smk /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nextstrain/ncov-ingest/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/dependabot.yml: 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