{"id":18289642,"url":"https://github.com/neherlab/nextclade_data_workflows","last_synced_at":"2025-08-01T03:08:39.055Z","repository":{"id":40592387,"uuid":"383262428","full_name":"neherlab/nextclade_data_workflows","owner":"neherlab","description":null,"archived":false,"fork":false,"pushed_at":"2025-07-24T09:25:33.000Z","size":7298,"stargazers_count":4,"open_issues_count":12,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-07-24T13:23:44.762Z","etag":null,"topics":["nextclade","nextstrain","phylogenetics","snakemake","virus-evolution"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/neherlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-07-05T20:55:57.000Z","updated_at":"2025-07-24T09:25:37.000Z","dependencies_parsed_at":"2022-08-24T23:40:24.973Z","dependency_job_id":"45b04df1-377b-435b-acc6-a479784d876d","html_url":"https://github.com/neherlab/nextclade_data_workflows","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/neherlab/nextclade_data_workflows","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neherlab%2Fnextclade_data_workflows","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neherlab%2Fnextclade_data_workflows/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neherlab%2Fnextclade_data_workflows/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neherlab%2Fnextclade_data_workflows/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/neherlab","download_url":"https://codeload.github.com/neherlab/nextclade_data_workflows/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neherlab%2Fnextclade_data_workflows/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268162399,"owners_count":24205702,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-01T02:00:08.611Z","response_time":67,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["nextclade","nextstrain","phylogenetics","snakemake","virus-evolution"],"created_at":"2024-11-05T14:07:25.858Z","updated_at":"2025-08-01T03:08:39.020Z","avatar_url":"https://github.com/neherlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Checking new tree\n\n1. Download generated files into nextclade data workflow repo:\n\n    ```bash\n    scp -rC roemer0001@login-transfer.scicore.unibas.ch:~/nextclade_data_workflows/sars-cov-2/output output\n    ```\n\n1. Plug them into nextclade.org advanced view.\n1. Filter to new nodes and check that:\n    - clades are clean\n    - no big outliers\n1. Check `tag.json` is up to date (ideally update in `profiles/tag.json` for posterity)\n1. Check `qc.json` does not regress (ideally update in `profiles/qc.json` for posterity) [beware, codons are 0 indexed]\n1. Potentially run `scripts/common_stops.py` and `scripts/common_frameshifts.py` to add new stops/frameshifts that have become more common to `qc.json`\n\n## Identifying most common frame shifts and stop conds\n\n1. Download metadata to `data/metadata_raw.tsv`\n1. Run snakemake workflow with following commands/targets:\n\n    ```bash\n    snakemake --profile=profiles/clades pre-processed/frameshifts.tsv -R select_frameshifts\n    snakemake --profile=profiles/clades pre-processed/stops.tsv -R select_stops\n    ```\n\n1. Format most commons stops/fs into qc.json JSON format using\n\n    ```bash\n    python3 scripts/common_stops.py\n    python3 scripts/common_frameshifts.py\n    ```\n\n1. Manually check resul for plausibility and add to qc.json\n\n\n## Committing to data repo\n\n1. Go to nextclade_data_workflow repo\n1. Checkout branch, open PR to master\n1. Copy output from workflow repo to data repo\n\n    ```bash\n    cp -r output/sars-cov-2/references/MN908947/versions/  ../../nextclade_data/data/datasets/sars-cov-2/references/MN908947/versions\n    ```\n\n1. Update `changelog.md`\n1. Get Ivan to review\n1. Merge into master\n\n## Release process\n\nFollow release guidelines as outlined here: https://github.com/nextstrain/nextclade_data#dataset-release-process\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneherlab%2Fnextclade_data_workflows","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fneherlab%2Fnextclade_data_workflows","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneherlab%2Fnextclade_data_workflows/lists"}