{"id":171438,"name":null,"description":"🧬  💻  TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission","url":"https://github.com/cdcgov/tostadas","last_synced_at":"2025-09-09T21:47:40.674Z","repository":{"id":54673675,"uuid":"522592754","full_name":"CDCgov/tostadas","owner":"CDCgov","description":"🧬  💻  TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission","archived":false,"fork":false,"pushed_at":"2025-09-05T15:38:45.000Z","size":51085,"stargazers_count":28,"open_issues_count":1,"forks_count":15,"subscribers_count":6,"default_branch":"dev","last_synced_at":"2025-09-05T17:45:59.133Z","etag":null,"topics":["azure","bioinformatics","conda","docker","genbank","genetics","liftoff","metadata","mpox","ncbi","nextflow","nf-tower","pipeline","python","rna-seq","scicomp","sequencing","singularity","sra","vadr"],"latest_commit_sha":null,"homepage":"https://cdcgov.github.io/tostadas/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/CDCgov.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"code-of-conduct.md","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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-08-08T14:55:05.000Z","updated_at":"2025-09-02T14:39:18.000Z","dependencies_parsed_at":"2023-11-29T16:49:56.157Z","dependency_job_id":"ad3216a3-50f9-4909-8135-b7634bce1c58","html_url":"https://github.com/CDCgov/tostadas","commit_stats":{"total_commits":594,"total_committers":6,"mean_commits":99.0,"dds":0.5202020202020202,"last_synced_commit":"19bb7391404d98e352d66cf7e4b0cadeece7cc97"},"previous_names":[],"tags_count":42,"template":false,"template_full_name":"CDCgov/template","purl":"pkg:github/CDCgov/tostadas","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Ftostadas","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Ftostadas/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Ftostadas/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Ftostadas/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CDCgov","download_url":"https://codeload.github.com/CDCgov/tostadas/tar.gz/refs/heads/dev","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Ftostadas/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274367587,"owners_count":25272297,"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":"2025-09-09T02:00:10.223Z","response_time":80,"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"}},"owner":{"login":"CDCgov","name":"Centers for Disease Control and Prevention","uuid":"12104975","kind":"organization","description":"CDC's collaborative software projects to protect America from health, safety, and security threats, both foreign and in the U.S.","email":"data@cdc.gov","website":"http://open.cdc.gov/","location":"Atlanta, GA","twitter":"CDCgov","company":null,"icon_url":"https://avatars.githubusercontent.com/u/12104975?v=4","repositories_count":114,"last_synced_at":"2023-03-01T17:45:31.221Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/CDCgov","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-12T14:08:08.128Z","updated_at":"2023-03-01T17:45:31.316Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CDCgov","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CDCgov/repositories"},"packages":null,"commits":{"id":1388878,"full_name":"cdcgov/tostadas","default_branch":"master","committers":[{"name":"ankushkgupta2","email":"ankushkgupta@deloitte.com","login":null,"count":285},{"name":"Cole tindall","email":"113549262+CTindall-1","login":"CTindall-1","count":200},{"name":"Gupta","email":"ufl1@biolinux.biotech.cdc.gov","login":null,"count":67},{"name":"Gupta","email":"ufl1@cdc.gov","login":null,"count":34},{"name":"Swarnali Louha","email":"142609937+Swarnali3","login":"Swarnali3","count":6},{"name":"Kyle O'Connell","email":"84786080+kyleoconnell","login":"kyleoconnell","count":2}],"total_commits":594,"total_committers":6,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":99.0,"dds":0.5202020202020202,"past_year_committers":[{"name":"ankushkgupta2","email":"ankushkgupta@deloitte.com","login":null,"count":285},{"name":"Cole tindall","email":"113549262+CTindall-1","login":"CTindall-1","count":200},{"name":"Gupta","email":"ufl1@biolinux.biotech.cdc.gov","login":null,"count":67},{"name":"Gupta","email":"ufl1@cdc.gov","login":null,"count":34},{"name":"Swarnali Louha","email":"142609937+Swarnali3","login":"Swarnali3","count":6},{"name":"Kyle O'Connell","email":"84786080+kyleoconnell","login":"kyleoconnell","count":2}],"past_year_total_commits":594,"past_year_total_committers":6,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":99.0,"past_year_dds":0.5202020202020202,"last_synced_at":"2024-01-25T19:36:16.454Z","last_synced_commit":"19bb7391404d98e352d66cf7e4b0cadeece7cc97","created_at":"2023-09-26T00:11:07.425Z","updated_at":"2024-01-25T19:36:16.455Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/cdcgov%2Ftostadas/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-07T00:00:09.744Z","repositories_count":5480019,"commits_count":853389126,"contributors_count":31098155,"owners_count":906558,"icon_url":"https://github.com/github.png","host_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories"}},"issues_stats":{"full_name":"cdcgov/tostadas","html_url":"https://github.com/cdcgov/tostadas","last_synced_at":"2025-08-31T07:51:18.922Z","status":null,"issues_count":179,"pull_requests_count":182,"avg_time_to_close_issue":6790337.197452229,"avg_time_to_close_pull_request":363517.12727272726,"issues_closed_count":157,"pull_requests_closed_count":165,"pull_request_authors_count":10,"issue_authors_count":21,"avg_comments_per_issue":0.6368715083798883,"avg_comments_per_pull_request":0.5,"merged_pull_requests_count":152,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":80,"past_year_pull_requests_count":83,"past_year_avg_time_to_close_issue":2756794.6612903224,"past_year_avg_time_to_close_pull_request":412253.2272727273,"past_year_issues_closed_count":62,"past_year_pull_requests_closed_count":66,"past_year_pull_request_authors_count":4,"past_year_issue_authors_count":10,"past_year_avg_comments_per_issue":0.5875,"past_year_avg_comments_per_pull_request":0.891566265060241,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":64,"created_at":"2023-09-26T00:11:38.180Z","updated_at":"2025-09-03T04:33:31.371Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/cdcgov%2Ftostadas","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/cdcgov%2Ftostadas/issues","issue_labels_count":{"enhancement":92,"bug":77,"implement":35,"documentation":14,"high-priority":11,"explore":9,"refactor":8,"testing-related":3,"testing":3,"internal":2,"good first issue":1,"frontend":1,"question":1},"pull_request_labels_count":{"bug":11,"enhancement":5,"documentation":4,"governance":1},"issue_author_associations_count":{"COLLABORATOR":153,"NONE":19,"CONTRIBUTOR":7},"pull_request_author_associations_count":{"COLLABORATOR":236,"NONE":2,"CONTRIBUTOR":2},"issue_authors":{"jessicarowell":59,"ankushkgupta2":55,"kyleoconnell":25,"RamiyapriyaS":13,"slsevilla":5,"kyleoconnell-CDC":2,"mikeyweigand":2,"Alan-Collins":2,"erinyoung":2,"jtakakuwa":2,"DOH-KEW4303":2,"Swarnali3":1,"lskatz":1,"krt7-cdc":1,"garfinjm":1,"jzm0-cdc":1,"nrminor":1,"mollymitchell70":1,"nbx0":1,"thomasphung":1,"ammaraziz":1},"pull_request_authors":{"jessicarowell":84,"ankushkgupta2":56,"RamiyapriyaS":46,"kyleoconnell":42,"Swarnali3":4,"macoven-del":2,"robsyme":2,"slsevilla":2,"Alan-Collins":1,"zyosufzai":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-09T00:00:11.778Z","repositories_count":10198054,"issues_count":32261643,"pull_requests_count":101813666,"authors_count":10741455,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{"bug":55,"enhancement":23},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"COLLABORATOR":74,"NONE":8},"past_year_pull_request_author_associations_count":{"COLLABORATOR":88,"NONE":1},"past_year_issue_authors":{"jessicarowell":55,"RamiyapriyaS":13,"slsevilla":5,"Alan-Collins":2,"DOH-KEW4303":2,"jzm0-cdc":1,"krt7-cdc":1,"kyleoconnell":1,"nrminor":1,"thomasphung":1},"past_year_pull_request_authors":{"jessicarowell":46,"RamiyapriyaS":40,"slsevilla":2,"Alan-Collins":1},"maintainers":[{"login":"jessicarowell","count":143,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jessicarowell"},{"login":"ankushkgupta2","count":103,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/ankushkgupta2"},{"login":"kyleoconnell","count":67,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/kyleoconnell"},{"login":"RamiyapriyaS","count":59,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/RamiyapriyaS"},{"login":"slsevilla","count":7,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/slsevilla"},{"login":"Swarnali3","count":5,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/Swarnali3"},{"login":"macoven-del","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/macoven-del"},{"login":"mikeyweigand","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mikeyweigand"},{"login":"zyosufzai","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/zyosufzai"}],"active_maintainers":[{"login":"jessicarowell","count":101,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jessicarowell"},{"login":"RamiyapriyaS","count":53,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/RamiyapriyaS"},{"login":"slsevilla","count":7,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/slsevilla"},{"login":"kyleoconnell","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/kyleoconnell"}]},"events":null,"keywords":["azure","bioinformatics","conda","docker","genbank","genetics","liftoff","metadata","mpox","ncbi","nextflow","nf-tower","pipeline","python","rna-seq","scicomp","sequencing","singularity","sra","vadr"],"dependencies":[{"ecosystem":"docker","filepath":"app/docker/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-02-18T03:16:14.293Z","updated_at":"2023-02-18T03:16:14.293Z","repository_link":"https://github.com/CDCgov/tostadas/blob/dev/app/docker/Dockerfile","dependencies":[{"id":7752650960,"package_name":"nfcore/base","ecosystem":"docker","requirements":"1.13.3","direct":true,"kind":"build","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/CI_main.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T16:25:23.781Z","updated_at":"2023-10-11T16:25:23.781Z","repository_link":"https://github.com/CDCgov/tostadas/blob/dev/.github/workflows/CI_main.yml","dependencies":[{"id":14153119256,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":14153119257,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"pypi","filepath":"environment.yml","sha":null,"kind":"manifest","created_at":"2023-11-29T16:49:54.493Z","updated_at":"2023-11-29T16:49:54.493Z","repository_link":"https://github.com/CDCgov/tostadas/blob/dev/environment.yml","dependencies":[]}],"score":5.159055299214529,"created_at":"2025-09-09T01:28:27.292Z","updated_at":"2025-10-07T08:39:58.580Z","avatar_url":"https://github.com/CDCgov.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/171438","html_url":"https://science.ecosyste.ms/projects/171438"}