{"id":56096,"name":"fetchdatairidanext","description":"Pipeline for downloading data from INSDC databases for IRIDA Next.","url":"https://github.com/phac-nml/fetchdatairidanext","last_synced_at":"2025-09-05T14:07:01.130Z","repository":{"id":218436860,"uuid":"739872714","full_name":"phac-nml/fetchdatairidanext","owner":"phac-nml","description":"Pipeline for downloading data from INSDC databases for IRIDA Next.","archived":false,"fork":false,"pushed_at":"2025-02-28T17:39:31.000Z","size":2659,"stargazers_count":0,"open_issues_count":2,"forks_count":2,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-02-28T20:49:04.980Z","etag":null,"topics":[],"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/phac-nml.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"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}},"created_at":"2024-01-06T19:57:07.000Z","updated_at":"2025-02-28T17:37:32.000Z","dependencies_parsed_at":"2024-04-09T20:43:11.184Z","dependency_job_id":"c59ff85c-c1fc-42ec-9f4b-7916d5b0a961","html_url":"https://github.com/phac-nml/fetchdatairidanext","commit_stats":null,"previous_names":["phac-nml/fetchdatairidanext"],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/phac-nml/fetchdatairidanext","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/phac-nml%2Ffetchdatairidanext","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/phac-nml%2Ffetchdatairidanext/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/phac-nml%2Ffetchdatairidanext/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/phac-nml%2Ffetchdatairidanext/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/phac-nml","download_url":"https://codeload.github.com/phac-nml/fetchdatairidanext/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/phac-nml%2Ffetchdatairidanext/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273768124,"owners_count":25164465,"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":"phac-nml","name":"National Microbiology Laboratory","uuid":"15620262","kind":"organization","description":"","email":null,"website":"https://www.nml-lnm.gc.ca/","location":null,"twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/15620262?v=4","repositories_count":50,"last_synced_at":"2023-04-01T07:09:53.442Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/phac-nml","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-04T09:11:32.384Z","updated_at":"2023-04-01T07:09:53.777Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/phac-nml","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/phac-nml/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"phac-nml/fetchdatairidanext","html_url":"https://github.com/phac-nml/fetchdatairidanext","last_synced_at":"2025-08-31T15:20:12.412Z","status":null,"issues_count":1,"pull_requests_count":7,"avg_time_to_close_issue":884166.0,"avg_time_to_close_pull_request":261430.14285714287,"issues_closed_count":1,"pull_requests_closed_count":7,"pull_request_authors_count":2,"issue_authors_count":1,"avg_comments_per_issue":1.0,"avg_comments_per_pull_request":1.4285714285714286,"merged_pull_requests_count":7,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":1,"past_year_pull_requests_count":7,"past_year_avg_time_to_close_issue":884166.0,"past_year_avg_time_to_close_pull_request":261430.14285714287,"past_year_issues_closed_count":1,"past_year_pull_requests_closed_count":7,"past_year_pull_request_authors_count":2,"past_year_issue_authors_count":1,"past_year_avg_comments_per_issue":1.0,"past_year_avg_comments_per_pull_request":1.4285714285714286,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":7,"created_at":"2025-08-30T14:44:17.616Z","updated_at":"2025-09-02T21:51:01.878Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/phac-nml%2Ffetchdatairidanext","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/phac-nml%2Ffetchdatairidanext/issues","issue_labels_count":{"enhancement":2,"bug":1},"pull_request_labels_count":{},"issue_author_associations_count":{"MEMBER":2,"NONE":1},"pull_request_author_associations_count":{"MEMBER":20,"NONE":2,"COLLABORATOR":2},"issue_authors":{"apetkau":2,"mcook19":1},"pull_request_authors":{"apetkau":16,"emarinier":3,"sgsutcliffe":2,"kylacochrane":2,"DarianHole":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10100117,"issues_count":31473266,"pull_requests_count":97445500,"authors_count":10702683,"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":1},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"MEMBER":1},"past_year_pull_request_author_associations_count":{"MEMBER":7,"NONE":2},"past_year_issue_authors":{"apetkau":1},"past_year_pull_request_authors":{"apetkau":6,"sgsutcliffe":2,"DarianHole":1},"maintainers":[{"login":"apetkau","count":18,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/apetkau"},{"login":"emarinier","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/emarinier"},{"login":"kylacochrane","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/kylacochrane"},{"login":"DarianHole","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/DarianHole"}],"active_maintainers":[{"login":"apetkau","count":7,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/apetkau"},{"login":"DarianHole","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/DarianHole"}]},"events":{"total":{"CreateEvent":9,"IssuesEvent":2,"ReleaseEvent":4,"DeleteEvent":4,"IssueCommentEvent":15,"PushEvent":49,"PullRequestReviewCommentEvent":49,"PullRequestReviewEvent":45,"PullRequestEvent":16,"ForkEvent":1},"last_year":{"CreateEvent":9,"IssuesEvent":2,"ReleaseEvent":4,"DeleteEvent":4,"IssueCommentEvent":15,"PushEvent":49,"PullRequestReviewCommentEvent":49,"PullRequestReviewEvent":45,"PullRequestEvent":16,"ForkEvent":1}},"keywords":[],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2024-01-21T23:45:19.960Z","updated_at":"2024-01-21T23:45:19.960Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/.github/workflows/branch.yml","dependencies":[{"id":15749203738,"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":"2024-01-21T23:45:20.020Z","updated_at":"2024-01-21T23:45:20.020Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/.github/workflows/ci.yml","dependencies":[{"id":15749203748,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":15749203749,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":15749204119,"package_name":"actions/cache","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting.yml","sha":null,"kind":"manifest","created_at":"2024-01-21T23:45:20.945Z","updated_at":"2024-01-21T23:45:20.945Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/.github/workflows/linting.yml","dependencies":[{"id":15749204120,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":15749204121,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":15749204122,"package_name":"psf/black","ecosystem":"actions","requirements":"stable","direct":true,"kind":"composite","optional":false},{"id":15749204123,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":15749204124,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":15749204125,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":15749204126,"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":"2024-01-21T23:45:20.955Z","updated_at":"2024-01-21T23:45:20.955Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/.github/workflows/linting_comment.yml","dependencies":[{"id":15749204127,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":15749204534,"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":"2024-01-21T23:45:21.964Z","updated_at":"2024-01-21T23:45:21.964Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/modules/nf-core/custom/dumpsoftwareversions/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2024-01-21T23:45:21.979Z","updated_at":"2024-01-21T23:45:21.979Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/pyproject.toml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/local/sratools/fasterqdump/meta.yml","sha":null,"kind":"manifest","created_at":"2024-02-22T22:48:15.796Z","updated_at":"2024-02-22T22:48:15.796Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/modules/local/sratools/fasterqdump/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/custom/sratoolsncbisettings/meta.yml","sha":null,"kind":"manifest","created_at":"2024-02-22T22:48:15.888Z","updated_at":"2024-02-22T22:48:15.888Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/modules/nf-core/custom/sratoolsncbisettings/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/sratools/prefetch/meta.yml","sha":null,"kind":"manifest","created_at":"2024-02-22T22:48:15.903Z","updated_at":"2024-02-22T22:48:15.903Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/modules/nf-core/sratools/prefetch/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/local/fastq_download_prefetch_fasterqdump_sratools/meta.yml","sha":null,"kind":"manifest","created_at":"2024-02-22T22:48:15.918Z","updated_at":"2024-02-22T22:48:15.918Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/subworkflows/local/fastq_download_prefetch_fasterqdump_sratools/meta.yml","dependencies":[]},{"ecosystem":"conda","filepath":"modules/local/sratools/fasterqdump/environment.yml","sha":null,"kind":"manifest","created_at":"2024-04-09T20:43:08.088Z","updated_at":"2024-04-09T20:43:08.088Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/modules/local/sratools/fasterqdump/environment.yml","dependencies":[{"id":17334074468,"package_name":"pigz","ecosystem":"conda","requirements":"2.6.*","direct":true,"kind":"runtime","optional":false},{"id":17334074469,"package_name":"sra-tools","ecosystem":"conda","requirements":"3.0.8.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/custom/sratoolsncbisettings/environment.yml","sha":null,"kind":"manifest","created_at":"2024-04-09T20:43:09.169Z","updated_at":"2024-04-09T20:43:09.169Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/modules/nf-core/custom/sratoolsncbisettings/environment.yml","dependencies":[{"id":17334074494,"package_name":"sra-tools","ecosystem":"conda","requirements":"3.0.8.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/sratools/prefetch/environment.yml","sha":null,"kind":"manifest","created_at":"2024-04-09T20:43:09.568Z","updated_at":"2024-04-09T20:43:09.568Z","repository_link":"https://github.com/phac-nml/fetchdatairidanext/blob/main/modules/nf-core/sratools/prefetch/environment.yml","dependencies":[{"id":17334074652,"package_name":"sra-tools","ecosystem":"conda","requirements":"3.0.8.*","direct":true,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-04T15:51:32.229Z","updated_at":"2025-10-07T08:22:10.566Z","avatar_url":"https://github.com/phac-nml.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/56096","html_url":"https://science.ecosyste.ms/projects/56096","bibtex_url":"https://science.ecosyste.ms/projects/56096/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/56096/export.apalike"}