{"id":29904841,"url":"https://github.com/andersen-lab/flusra","last_synced_at":"2026-02-09T11:03:54.758Z","repository":{"id":240284344,"uuid":"800847854","full_name":"andersen-lab/flusra","owner":"andersen-lab","description":null,"archived":false,"fork":false,"pushed_at":"2025-05-15T01:20:57.000Z","size":1314,"stargazers_count":3,"open_issues_count":2,"forks_count":4,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-07-28T06:31:19.687Z","etag":null,"topics":["flu"],"latest_commit_sha":null,"homepage":"","language":"Nextflow","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/andersen-lab.png","metadata":{"files":{"readme":"docs/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":"2024-05-15T05:44:23.000Z","updated_at":"2025-05-15T00:19:45.000Z","dependencies_parsed_at":"2024-06-07T04:49:24.522Z","dependency_job_id":"6c6ca8cb-8339-480a-b9a2-ec32ff83ae30","html_url":"https://github.com/andersen-lab/flusra","commit_stats":null,"previous_names":["gp201/sra","gp201/flusra"],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/andersen-lab/flusra","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andersen-lab%2Fflusra","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andersen-lab%2Fflusra/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andersen-lab%2Fflusra/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andersen-lab%2Fflusra/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/andersen-lab","download_url":"https://codeload.github.com/andersen-lab/flusra/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andersen-lab%2Fflusra/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268273446,"owners_count":24223796,"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":["flu"],"created_at":"2025-08-01T18:16:01.218Z","updated_at":"2026-02-09T11:03:49.695Z","avatar_url":"https://github.com/andersen-lab.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# flusra: Documentation\n\nYou can run the pipeline with the following command:\n\n```bash\nnextflow run https://github.com/andersen-lab/flusra.git -r 'main' -c /nextflow.config -profile \u003cmamba,conda\u003e\n```\n\n## Parameters in the `nextflow.config` file\n\n- `bioproject`: The BioProject ID to fetch the data from NCBI.\n- `email`: The email address to use for the NCBI API.\n- `only_fetch`: If `true`, only fetch the metadata from NCBI and save it to the `outdir` directory.\n- `fetch_and_pull`: If `true`, fetch the metadata from NCBI and pulls the new data from SRA.\n- `metadata`: Provide an existing metadata file to bypass processing already processed SRA data\n- `reference`: The reference genome to use for mapping.\n- `sra_accessions`: The SRA accessions to process. Provide a list of SRA accessions to process without a BioProject ID skips fetching metadata.\n- `outdir`: The output directory where the results will be saved.\n\nIf you want to run the pipeline with a different configuration, you can create a new `nextflow.config` file and provide the path to the `-c` option.\n\nPlease report any issues and suggestions regarding the pipeline to the [issue tracker](https://github.com/andersen-lab/flusra/issues).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandersen-lab%2Fflusra","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fandersen-lab%2Fflusra","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandersen-lab%2Fflusra/lists"}