{"id":30971,"name":"phylophoenix","description":"🔥🌿🐦🔥PhyloPHoeNIx: Pipeline for relatedness determination using PHoeNIx output.","url":"https://github.com/cdcgov/phylophoenix","last_synced_at":"2025-09-05T05:01:09.608Z","repository":{"id":298567222,"uuid":"889135033","full_name":"CDCgov/phylophoenix","owner":"CDCgov","description":"🔥🌿🐦🔥PhyloPHoeNIx: Pipeline for relatedness determination using PHoeNIx output.","archived":false,"fork":false,"pushed_at":"2025-08-29T00:51:41.000Z","size":160042,"stargazers_count":6,"open_issues_count":3,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-08-29T05:28:11.927Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://www.cdc.gov/ncezid/divisions-offices/about-dhqp.html","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":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATIONS.md","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2024-11-15T17:17:14.000Z","updated_at":"2025-07-21T22:29:59.000Z","dependencies_parsed_at":"2025-08-12T02:39:34.659Z","dependency_job_id":null,"html_url":"https://github.com/CDCgov/phylophoenix","commit_stats":null,"previous_names":["cdcgov/phylophoenix"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/CDCgov/phylophoenix","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fphylophoenix","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fphylophoenix/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fphylophoenix/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fphylophoenix/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CDCgov","download_url":"https://codeload.github.com/CDCgov/phylophoenix/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fphylophoenix/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273713605,"owners_count":25154612,"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":"2025-09-05T02:00:09.113Z","response_time":402,"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":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"CDCgov/phylophoenix","html_url":"https://github.com/CDCgov/phylophoenix","last_synced_at":null,"status":null,"issues_count":null,"pull_requests_count":null,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":null,"issues_closed_count":null,"pull_requests_closed_count":null,"pull_request_authors_count":null,"issue_authors_count":null,"avg_comments_per_issue":null,"avg_comments_per_pull_request":null,"merged_pull_requests_count":null,"bot_issues_count":null,"bot_pull_requests_count":null,"past_year_issues_count":null,"past_year_pull_requests_count":null,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":null,"past_year_issues_closed_count":null,"past_year_pull_requests_closed_count":null,"past_year_pull_request_authors_count":null,"past_year_issue_authors_count":null,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":null,"past_year_bot_issues_count":null,"past_year_bot_pull_requests_count":null,"past_year_merged_pull_requests_count":null,"created_at":"2025-08-29T13:45:58.799Z","updated_at":"2025-08-29T18:21:22.811Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fphylophoenix","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fphylophoenix/issues","issue_labels_count":{"bug":2},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":1,"COLLABORATOR":1},"pull_request_author_associations_count":{"COLLABORATOR":1},"issue_authors":{"jenniferlu717":1,"nvlachos":1},"pull_request_authors":{"jvhagey":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10086361,"issues_count":31286210,"pull_requests_count":96411606,"authors_count":10695498,"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":2},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"COLLABORATOR":1,"NONE":1},"past_year_pull_request_author_associations_count":{"COLLABORATOR":1},"past_year_issue_authors":{"jenniferlu717":1,"nvlachos":1},"past_year_pull_request_authors":{"jvhagey":1},"maintainers":[{"login":"jvhagey","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jvhagey"},{"login":"nvlachos","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nvlachos"}],"active_maintainers":[{"login":"jvhagey","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/jvhagey"},{"login":"nvlachos","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nvlachos"}]},"events":{"total":{"CreateEvent":4,"IssuesEvent":3,"ReleaseEvent":2,"WatchEvent":5,"IssueCommentEvent":6,"MemberEvent":1,"PushEvent":54,"PublicEvent":1,"PullRequestEvent":2,"GollumEvent":1},"last_year":{"CreateEvent":4,"IssuesEvent":3,"ReleaseEvent":2,"WatchEvent":5,"IssueCommentEvent":6,"MemberEvent":1,"PushEvent":54,"PublicEvent":1,"PullRequestEvent":2,"GollumEvent":1}},"keywords":[],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/awsfulltest.yml","sha":null,"kind":"manifest","created_at":"2025-06-19T01:40:37.822Z","updated_at":"2025-06-19T01:40:37.822Z","repository_link":"https://github.com/CDCgov/phylophoenix/blob/main/.github/workflows/awsfulltest.yml","dependencies":[{"id":23694756273,"package_name":"nf-core/tower-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":23694756741,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/awstest.yml","sha":null,"kind":"manifest","created_at":"2025-06-19T01:40:39.396Z","updated_at":"2025-06-19T01:40:39.396Z","repository_link":"https://github.com/CDCgov/phylophoenix/blob/main/.github/workflows/awstest.yml","dependencies":[{"id":23694756742,"package_name":"nf-core/tower-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":23694756743,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2025-06-19T01:40:39.452Z","updated_at":"2025-06-19T01:40:39.452Z","repository_link":"https://github.com/CDCgov/phylophoenix/blob/main/.github/workflows/branch.yml","dependencies":[{"id":23694757126,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/ci.yml","sha":null,"kind":"manifest","created_at":"2025-06-19T01:40:39.509Z","updated_at":"2025-06-19T01:40:39.509Z","repository_link":"https://github.com/CDCgov/phylophoenix/blob/main/.github/workflows/ci.yml","dependencies":[{"id":23694757177,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":23694757178,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/fix-linting.yml","sha":null,"kind":"manifest","created_at":"2025-06-19T01:40:41.130Z","updated_at":"2025-06-19T01:40:41.130Z","repository_link":"https://github.com/CDCgov/phylophoenix/blob/main/.github/workflows/fix-linting.yml","dependencies":[{"id":23694758641,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":23694758642,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting.yml","sha":null,"kind":"manifest","created_at":"2025-06-19T01:40:41.297Z","updated_at":"2025-06-19T01:40:41.297Z","repository_link":"https://github.com/CDCgov/phylophoenix/blob/main/.github/workflows/linting.yml","dependencies":[{"id":23694758656,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":23694758657,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":23694758658,"package_name":"psf/black","ecosystem":"actions","requirements":"stable","direct":true,"kind":"composite","optional":false},{"id":23694759008,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":23694759009,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":23694759010,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":23694759011,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting_comment.yml","sha":null,"kind":"manifest","created_at":"2025-06-19T01:40:43.066Z","updated_at":"2025-06-19T01:40:43.066Z","repository_link":"https://github.com/CDCgov/phylophoenix/blob/main/.github/workflows/linting_comment.yml","dependencies":[{"id":23694759055,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":23694759056,"package_name":"marocchino/sticky-pull-request-comment","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/update_clone_badge.yml","sha":null,"kind":"manifest","created_at":"2025-06-19T01:40:43.122Z","updated_at":"2025-06-19T01:40:43.122Z","repository_link":"https://github.com/CDCgov/phylophoenix/blob/main/.github/workflows/update_clone_badge.yml","dependencies":[{"id":23694759061,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/custom/dumpsoftwareversions/meta.yml","sha":null,"kind":"manifest","created_at":"2025-07-06T02:28:30.247Z","updated_at":"2025-07-06T02:28:30.247Z","repository_link":"https://github.com/CDCgov/phylophoenix/blob/main/modules/nf-core/custom/dumpsoftwareversions/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastqc/meta.yml","sha":null,"kind":"manifest","created_at":"2025-07-06T02:28:30.287Z","updated_at":"2025-07-06T02:28:30.287Z","repository_link":"https://github.com/CDCgov/phylophoenix/blob/main/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2025-07-06T02:28:30.327Z","updated_at":"2025-07-06T02:28:30.327Z","repository_link":"https://github.com/CDCgov/phylophoenix/blob/main/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2025-07-06T02:28:30.367Z","updated_at":"2025-07-06T02:28:30.367Z","repository_link":"https://github.com/CDCgov/phylophoenix/blob/main/pyproject.toml","dependencies":[]}],"score":null,"created_at":"2025-09-04T15:51:03.782Z","updated_at":"2025-10-07T08:13:17.442Z","avatar_url":"https://github.com/CDCgov.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.15643996","https://doi.org/10.5281/zenodo.XXXXXX","https://dx.doi.org/10.1038/s41587-020-0439-x"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/30971","html_url":"https://science.ecosyste.ms/projects/30971"}