{"id":23675,"name":"ensemblrepeatdownload","description":"Nextflow DSL2 pipeline to download repeat annotations from Ensembl.","url":"https://github.com/sanger-tol/ensemblrepeatdownload","last_synced_at":"2025-09-05T02:06:00.377Z","repository":{"id":61671783,"uuid":"541153820","full_name":"sanger-tol/ensemblrepeatdownload","owner":"sanger-tol","description":"Nextflow DSL2 pipeline to download repeat annotations from Ensembl.","archived":false,"fork":false,"pushed_at":"2025-08-19T12:49:18.000Z","size":2651,"stargazers_count":1,"open_issues_count":6,"forks_count":1,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-08-19T14:46:50.007Z","etag":null,"topics":["download","formatting","genomics","nextflow","pipeline"],"latest_commit_sha":null,"homepage":"https://pipelines.tol.sanger.ac.uk/ensemblrepeatdownload","language":"Groovy","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/sanger-tol.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":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-09-25T11:50:55.000Z","updated_at":"2025-05-12T23:01:40.000Z","dependencies_parsed_at":"2025-08-19T14:31:03.327Z","dependency_job_id":"51d77d00-d5b9-4687-a75a-a8b74376b144","html_url":"https://github.com/sanger-tol/ensemblrepeatdownload","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/sanger-tol/ensemblrepeatdownload","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fensemblrepeatdownload","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fensemblrepeatdownload/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fensemblrepeatdownload/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fensemblrepeatdownload/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sanger-tol","download_url":"https://codeload.github.com/sanger-tol/ensemblrepeatdownload/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fensemblrepeatdownload/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273699712,"owners_count":25152286,"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":"sanger-tol","name":"Tree of Life programme","uuid":"70318076","kind":"organization","description":"The Tree of Life Programme investigates the diversity of complex organisms (eukaryotes) through sequencing and cellular technology","email":null,"website":"https://www.sanger.ac.uk/programme/tree-of-life/","location":"United Kingdom","twitter":"sangertol","company":null,"icon_url":"https://avatars.githubusercontent.com/u/70318076?v=4","repositories_count":15,"last_synced_at":"2023-03-04T17:33:58.308Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/sanger-tol","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-14T21:51:33.911Z","updated_at":"2023-03-04T17:33:58.332Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sanger-tol","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sanger-tol/repositories"},"packages":null,"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"sanger-tol/ensemblrepeatdownload","html_url":"https://github.com/sanger-tol/ensemblrepeatdownload","last_synced_at":"2025-08-31T19:34:16.941Z","status":null,"issues_count":2,"pull_requests_count":2,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":250174.0,"issues_closed_count":0,"pull_requests_closed_count":1,"pull_request_authors_count":2,"issue_authors_count":1,"avg_comments_per_issue":0.0,"avg_comments_per_pull_request":1.0,"merged_pull_requests_count":1,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":2,"past_year_pull_requests_count":2,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":250174.0,"past_year_issues_closed_count":0,"past_year_pull_requests_closed_count":1,"past_year_pull_request_authors_count":2,"past_year_issue_authors_count":1,"past_year_avg_comments_per_issue":0.0,"past_year_avg_comments_per_pull_request":1.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":1,"created_at":"2025-08-29T14:50:05.609Z","updated_at":"2025-09-03T02:09:41.258Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fensemblrepeatdownload","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fensemblrepeatdownload/issues","issue_labels_count":{"enhancement":1},"pull_request_labels_count":{"bug":1,"enhancement":1},"issue_author_associations_count":{"MEMBER":2},"pull_request_author_associations_count":{"MEMBER":3,"NONE":3,"CONTRIBUTOR":2},"issue_authors":{"muffato":2},"pull_request_authors":{"tkchafin":4,"muffato":2,"sanger-tolsoft":1,"gq1":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10082226,"issues_count":31213887,"pull_requests_count":96046612,"authors_count":10694202,"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":1},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"MEMBER":2},"past_year_pull_request_author_associations_count":{"NONE":3,"CONTRIBUTOR":2,"MEMBER":1},"past_year_issue_authors":{"muffato":2},"past_year_pull_request_authors":{"tkchafin":4,"muffato":1,"sanger-tolsoft":1},"maintainers":[{"login":"muffato","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/muffato"},{"login":"gq1","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/gq1"}],"active_maintainers":[{"login":"muffato","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/muffato"}]},"events":{"total":{"CreateEvent":6,"IssuesEvent":2,"ReleaseEvent":1,"DeleteEvent":5,"MemberEvent":1,"IssueCommentEvent":9,"PushEvent":10,"PullRequestReviewEvent":4,"PullRequestReviewCommentEvent":1,"PullRequestEvent":11,"ForkEvent":1},"last_year":{"CreateEvent":6,"IssuesEvent":2,"ReleaseEvent":1,"DeleteEvent":5,"MemberEvent":1,"IssueCommentEvent":9,"PushEvent":10,"PullRequestReviewEvent":4,"PullRequestReviewCommentEvent":1,"PullRequestEvent":11,"ForkEvent":1}},"keywords":["download","formatting","genomics","nextflow","pipeline"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2023-02-17T22:45:27.163Z","updated_at":"2023-02-17T22:45:27.163Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/.github/workflows/branch.yml","dependencies":[{"id":7747880564,"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":"2023-02-17T22:45:27.273Z","updated_at":"2023-02-17T22:45:27.273Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/.github/workflows/ci.yml","dependencies":[{"id":7747880958,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7747880959,"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":"2023-02-17T22:45:27.443Z","updated_at":"2023-02-17T22:45:27.443Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/.github/workflows/fix-linting.yml","dependencies":[{"id":7747882758,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7747882759,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting.yml","sha":null,"kind":"manifest","created_at":"2023-02-17T22:45:27.557Z","updated_at":"2023-02-17T22:45:27.557Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/.github/workflows/linting.yml","dependencies":[{"id":7747882819,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7747882820,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7747882821,"package_name":"psf/black","ecosystem":"actions","requirements":"stable","direct":true,"kind":"composite","optional":false},{"id":7747882822,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7747882823,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7747882824,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7747882825,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting_comment.yml","sha":null,"kind":"manifest","created_at":"2023-02-17T22:45:27.646Z","updated_at":"2023-02-17T22:45:27.646Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/.github/workflows/linting_comment.yml","dependencies":[{"id":7747883109,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7747883110,"package_name":"marocchino/sticky-pull-request-comment","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/clean-up.yml","sha":null,"kind":"manifest","created_at":"2024-12-05T22:35:07.198Z","updated_at":"2024-12-05T22:35:07.198Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/.github/workflows/clean-up.yml","dependencies":[{"id":21053331404,"package_name":"actions/stale","ecosystem":"actions","requirements":"v7","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/sanger_test.yml","sha":null,"kind":"manifest","created_at":"2024-12-05T22:35:07.312Z","updated_at":"2024-12-05T22:35:07.312Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/.github/workflows/sanger_test.yml","dependencies":[{"id":21053331408,"package_name":"seqeralabs/action-tower-launch","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":21053331409,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/sanger_test_full.yml","sha":null,"kind":"manifest","created_at":"2024-12-05T22:35:07.384Z","updated_at":"2024-12-05T22:35:07.384Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/.github/workflows/sanger_test_full.yml","dependencies":[{"id":21053331415,"package_name":"seqeralabs/action-tower-launch","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":21053331416,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/custom/dumpsoftwareversions/meta.yml","sha":null,"kind":"manifest","created_at":"2024-12-05T22:35:07.456Z","updated_at":"2024-12-05T22:35:07.456Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/modules/nf-core/custom/dumpsoftwareversions/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/custom/getchromsizes/meta.yml","sha":null,"kind":"manifest","created_at":"2024-12-05T22:35:07.500Z","updated_at":"2024-12-05T22:35:07.500Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/modules/nf-core/custom/getchromsizes/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/dict/meta.yml","sha":null,"kind":"manifest","created_at":"2024-12-05T22:35:07.544Z","updated_at":"2024-12-05T22:35:07.544Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/modules/nf-core/samtools/dict/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/faidx/meta.yml","sha":null,"kind":"manifest","created_at":"2024-12-05T22:35:07.587Z","updated_at":"2024-12-05T22:35:07.587Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/modules/nf-core/samtools/faidx/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tabix/bgzip/meta.yml","sha":null,"kind":"manifest","created_at":"2024-12-05T22:35:07.631Z","updated_at":"2024-12-05T22:35:07.631Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/modules/nf-core/tabix/bgzip/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tabix/tabix/meta.yml","sha":null,"kind":"manifest","created_at":"2024-12-05T22:35:07.675Z","updated_at":"2024-12-05T22:35:07.675Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/modules/nf-core/tabix/tabix/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2024-12-05T22:35:07.725Z","updated_at":"2024-12-05T22:35:07.725Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/pyproject.toml","dependencies":[]},{"ecosystem":"conda","filepath":"modules/nf-core/custom/dumpsoftwareversions/environment.yml","sha":null,"kind":"manifest","created_at":"2025-08-19T14:30:54.379Z","updated_at":"2025-08-19T14:30:54.379Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/modules/nf-core/custom/dumpsoftwareversions/environment.yml","dependencies":[{"id":24744356017,"package_name":"multiqc","ecosystem":"conda","requirements":"1.20.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/samtools/dict/environment.yml","sha":null,"kind":"manifest","created_at":"2025-08-19T14:30:55.086Z","updated_at":"2025-08-19T14:30:55.086Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/modules/nf-core/samtools/dict/environment.yml","dependencies":[{"id":24744356018,"package_name":"htslib","ecosystem":"conda","requirements":"1.21.*","direct":true,"kind":"runtime","optional":false},{"id":24744356050,"package_name":"samtools","ecosystem":"conda","requirements":"1.21.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/samtools/faidx/environment.yml","sha":null,"kind":"manifest","created_at":"2025-08-19T14:30:56.379Z","updated_at":"2025-08-19T14:30:56.379Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/modules/nf-core/samtools/faidx/environment.yml","dependencies":[{"id":24744356053,"package_name":"htslib","ecosystem":"conda","requirements":"1.21.*","direct":true,"kind":"runtime","optional":false},{"id":24744356054,"package_name":"samtools","ecosystem":"conda","requirements":"1.21.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/tabix/bgzip/environment.yml","sha":null,"kind":"manifest","created_at":"2025-08-19T14:30:56.497Z","updated_at":"2025-08-19T14:30:56.497Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/modules/nf-core/tabix/bgzip/environment.yml","dependencies":[{"id":24744356221,"package_name":"htslib","ecosystem":"conda","requirements":"1.20.*","direct":true,"kind":"runtime","optional":false},{"id":24744356222,"package_name":"tabix","ecosystem":"conda","requirements":"1.11.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/tabix/tabix/environment.yml","sha":null,"kind":"manifest","created_at":"2025-08-19T14:30:59.814Z","updated_at":"2025-08-19T14:30:59.814Z","repository_link":"https://github.com/sanger-tol/ensemblrepeatdownload/blob/main/modules/nf-core/tabix/tabix/environment.yml","dependencies":[{"id":24744356877,"package_name":"htslib","ecosystem":"conda","requirements":"1.20.*","direct":true,"kind":"runtime","optional":false},{"id":24744356879,"package_name":"tabix","ecosystem":"conda","requirements":"1.11.*","direct":true,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-04T15:50:55.416Z","updated_at":"2025-10-07T08:11:01.720Z","avatar_url":"https://github.com/sanger-tol.png","language":"Groovy","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.7183379","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/23675","html_url":"https://science.ecosyste.ms/projects/23675","bibtex_url":"https://science.ecosyste.ms/projects/23675/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/23675/export.apalike"}