{"id":32420,"name":"bigbacter-nf","description":"Bacterial surveillance pipeline.","url":"https://github.com/doh-jdj0303/bigbacter-nf","last_synced_at":"2025-09-05T05:26:45.892Z","repository":{"id":189036467,"uuid":"654739731","full_name":"DOH-JDJ0303/bigbacter-nf","owner":"DOH-JDJ0303","description":"Bacterial surveillance pipeline.","archived":false,"fork":false,"pushed_at":"2025-05-13T18:56:03.000Z","size":7027,"stargazers_count":24,"open_issues_count":4,"forks_count":4,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-05-13T19:55:12.952Z","etag":null,"topics":["accessory-genome","bacterial-genomics","clustering-analysis","genome-analysis","public-health","public-health-surveillance","snp-analysis"],"latest_commit_sha":null,"homepage":"","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/DOH-JDJ0303.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":"2023-06-16T20:43:00.000Z","updated_at":"2025-03-12T16:10:32.000Z","dependencies_parsed_at":"2023-08-18T00:55:28.217Z","dependency_job_id":"8e8741fe-de42-4dee-bab7-e6f8cc67d62a","html_url":"https://github.com/DOH-JDJ0303/bigbacter-nf","commit_stats":null,"previous_names":["doh-jdj0303/bigbacter-nf"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/DOH-JDJ0303/bigbacter-nf","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DOH-JDJ0303%2Fbigbacter-nf","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DOH-JDJ0303%2Fbigbacter-nf/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DOH-JDJ0303%2Fbigbacter-nf/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DOH-JDJ0303%2Fbigbacter-nf/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DOH-JDJ0303","download_url":"https://codeload.github.com/DOH-JDJ0303/bigbacter-nf/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DOH-JDJ0303%2Fbigbacter-nf/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273714233,"owners_count":25154774,"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":"DOH-JDJ0303","name":null,"uuid":"134550566","kind":"user","description":null,"email":"","website":null,"location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/134550566?u=f919f4087f9b83b37d31a3b3f73d098bb0a68c68\u0026v=4","repositories_count":1,"last_synced_at":"2023-06-09T21:26:01.570Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/DOH-JDJ0303","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-06-09T21:26:01.575Z","updated_at":"2023-06-09T21:26:01.575Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DOH-JDJ0303","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DOH-JDJ0303/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"DOH-JDJ0303/bigbacter-nf","html_url":"https://github.com/DOH-JDJ0303/bigbacter-nf","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":"2025-08-29T18:59:40.349Z","updated_at":"2025-09-03T03:16:52.225Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/DOH-JDJ0303%2Fbigbacter-nf","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/DOH-JDJ0303%2Fbigbacter-nf/issues","issue_labels_count":{"enhancement":6,"bug":4},"pull_request_labels_count":{},"issue_author_associations_count":{"OWNER":11,"NONE":3},"pull_request_author_associations_count":{"OWNER":6,"COLLABORATOR":4},"issue_authors":{"DOH-JDJ0303":11,"DOH-LMT2303":1,"hutchinsonmiri":1,"slsevilla":1},"pull_request_authors":{"DOH-JDJ0303":6,"DOH-HNH0303":4},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10086255,"issues_count":31275313,"pull_requests_count":96382867,"authors_count":10695584,"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":{"enhancement":6,"bug":2},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"OWNER":10,"NONE":2},"past_year_pull_request_author_associations_count":{"OWNER":4,"COLLABORATOR":4},"past_year_issue_authors":{"DOH-JDJ0303":10,"DOH-LMT2303":1,"hutchinsonmiri":1},"past_year_pull_request_authors":{"DOH-HNH0303":4,"DOH-JDJ0303":4},"maintainers":[{"login":"DOH-JDJ0303","count":17,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/DOH-JDJ0303"},{"login":"DOH-HNH0303","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/DOH-HNH0303"}],"active_maintainers":[{"login":"DOH-JDJ0303","count":14,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/DOH-JDJ0303"},{"login":"DOH-HNH0303","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/DOH-HNH0303"}]},"events":{"total":{"CreateEvent":9,"IssuesEvent":16,"ReleaseEvent":1,"WatchEvent":7,"DeleteEvent":5,"MemberEvent":1,"IssueCommentEvent":8,"PushEvent":20,"PullRequestEvent":12,"ForkEvent":1},"last_year":{"CreateEvent":9,"IssuesEvent":16,"ReleaseEvent":1,"WatchEvent":7,"DeleteEvent":5,"MemberEvent":1,"IssueCommentEvent":8,"PushEvent":20,"PullRequestEvent":12,"ForkEvent":1}},"keywords":["accessory-genome","bacterial-genomics","clustering-analysis","genome-analysis","public-health","public-health-surveillance","snp-analysis"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/awsfulltest.yml","sha":null,"kind":"manifest","created_at":"2023-08-18T00:55:27.088Z","updated_at":"2023-08-18T00:55:27.088Z","repository_link":"https://github.com/DOH-JDJ0303/bigbacter-nf/blob/main/.github/workflows/awsfulltest.yml","dependencies":[{"id":12762908477,"package_name":"seqeralabs/action-tower-launch","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":12762908478,"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":"2023-08-18T00:55:27.144Z","updated_at":"2023-08-18T00:55:27.144Z","repository_link":"https://github.com/DOH-JDJ0303/bigbacter-nf/blob/main/.github/workflows/awstest.yml","dependencies":[{"id":12762908479,"package_name":"seqeralabs/action-tower-launch","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":12762908480,"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":"2023-08-18T00:55:27.300Z","updated_at":"2023-08-18T00:55:27.300Z","repository_link":"https://github.com/DOH-JDJ0303/bigbacter-nf/blob/main/.github/workflows/branch.yml","dependencies":[{"id":12762908849,"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":"2023-08-18T00:55:27.362Z","updated_at":"2023-08-18T00:55:27.362Z","repository_link":"https://github.com/DOH-JDJ0303/bigbacter-nf/blob/main/.github/workflows/ci.yml","dependencies":[{"id":12762909433,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":12762909434,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/clean-up.yml","sha":null,"kind":"manifest","created_at":"2023-08-18T00:55:27.433Z","updated_at":"2023-08-18T00:55:27.433Z","repository_link":"https://github.com/DOH-JDJ0303/bigbacter-nf/blob/main/.github/workflows/clean-up.yml","dependencies":[{"id":12762910241,"package_name":"actions/stale","ecosystem":"actions","requirements":"v7","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/fix-linting.yml","sha":null,"kind":"manifest","created_at":"2023-08-18T00:55:27.500Z","updated_at":"2023-08-18T00:55:27.500Z","repository_link":"https://github.com/DOH-JDJ0303/bigbacter-nf/blob/main/.github/workflows/fix-linting.yml","dependencies":[{"id":12762910544,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":12762910545,"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":"2023-08-18T00:55:27.556Z","updated_at":"2023-08-18T00:55:27.556Z","repository_link":"https://github.com/DOH-JDJ0303/bigbacter-nf/blob/main/.github/workflows/linting.yml","dependencies":[{"id":12762910546,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":12762910547,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":12762910548,"package_name":"psf/black","ecosystem":"actions","requirements":"stable","direct":true,"kind":"composite","optional":false},{"id":12762910549,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":12762910550,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":12762910551,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":12762910552,"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":"2023-08-18T00:55:27.612Z","updated_at":"2023-08-18T00:55:27.612Z","repository_link":"https://github.com/DOH-JDJ0303/bigbacter-nf/blob/main/.github/workflows/linting_comment.yml","dependencies":[{"id":12762910573,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":12762910574,"package_name":"marocchino/sticky-pull-request-comment","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":"2023-08-18T00:55:27.789Z","updated_at":"2023-08-18T00:55:27.789Z","repository_link":"https://github.com/DOH-JDJ0303/bigbacter-nf/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":"2023-08-18T00:55:27.899Z","updated_at":"2023-08-18T00:55:27.899Z","repository_link":"https://github.com/DOH-JDJ0303/bigbacter-nf/blob/main/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2023-08-18T00:55:28.057Z","updated_at":"2023-08-18T00:55:28.057Z","repository_link":"https://github.com/DOH-JDJ0303/bigbacter-nf/blob/main/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2023-08-18T00:55:28.128Z","updated_at":"2023-08-18T00:55:28.128Z","repository_link":"https://github.com/DOH-JDJ0303/bigbacter-nf/blob/main/pyproject.toml","dependencies":[]}],"score":null,"created_at":"2025-09-04T15:51:05.507Z","updated_at":"2025-10-07T08:13:45.374Z","avatar_url":"https://github.com/DOH-JDJ0303.png","language":"Nextflow","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/32420","html_url":"https://science.ecosyste.ms/projects/32420","bibtex_url":"https://science.ecosyste.ms/projects/32420/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/32420/export.apalike"}