{"id":55597,"name":"arrakis","description":"Abra realignment workflow","url":"https://github.com/mskcc/arrakis","last_synced_at":"2025-09-05T13:57:08.012Z","repository":{"id":226090285,"uuid":"765839154","full_name":"mskcc/arrakis","owner":"mskcc","description":"Abra realignment workflow","archived":false,"fork":false,"pushed_at":"2024-11-13T15:22:49.000Z","size":333,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-02-28T08:28:12.056Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/mskcc.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":"2024-03-01T18:10:16.000Z","updated_at":"2024-04-15T15:36:12.000Z","dependencies_parsed_at":"2024-03-11T16:06:24.036Z","dependency_job_id":"f77cd893-6eee-4674-91d2-09847d6d0098","html_url":"https://github.com/mskcc/arrakis","commit_stats":null,"previous_names":["mskcc/arrakis"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/mskcc/arrakis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Farrakis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Farrakis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Farrakis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Farrakis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/arrakis/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Farrakis/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273768145,"owners_count":25164464,"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":"mskcc","name":"Memorial Sloan Kettering","uuid":"6900073","kind":"organization","description":"","email":"perinj@mskcc.org","website":"http://www.mskcc.org","location":"New York, NY, USA","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/6900073?v=4","repositories_count":188,"last_synced_at":"2023-08-06T05:32:01.444Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/mskcc","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-06T14:30:57.879Z","updated_at":"2023-08-06T05:32:01.861Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc/repositories"},"packages":[],"commits":{"id":5237286,"full_name":"mskcc/arrakis","default_branch":"master","committers":[{"name":"Nikhil Kumar","email":"nikhilkumar516@gmail.com","login":"nikhil","count":30},{"name":"Nicholas D. Socci","email":"soccin@mskcc.org","login":"soccin","count":1}],"total_commits":31,"total_committers":2,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":15.5,"dds":0.032258064516129004,"past_year_committers":[{"name":"Nikhil Kumar","email":"nikhilkumar516@gmail.com","login":"nikhil","count":30},{"name":"Nicholas D. Socci","email":"soccin@mskcc.org","login":"soccin","count":1}],"past_year_total_commits":31,"past_year_total_committers":2,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":15.5,"past_year_dds":0.032258064516129004,"last_synced_at":"2025-01-12T03:45:30.863Z","last_synced_commit":"a13d58c4cbd1f332759b04ef1717753f57fc2181","created_at":"2024-11-12T02:26:25.388Z","updated_at":"2025-01-12T03:45:30.864Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Farrakis/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.343Z","repositories_count":5480019,"commits_count":853389012,"contributors_count":31098138,"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":"mskcc/arrakis","html_url":"https://github.com/mskcc/arrakis","last_synced_at":"2025-02-28T00:40:31.561Z","status":null,"issues_count":1,"pull_requests_count":4,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":3791242.5,"issues_closed_count":0,"pull_requests_closed_count":4,"pull_request_authors_count":2,"issue_authors_count":1,"avg_comments_per_issue":0.0,"avg_comments_per_pull_request":0.0,"merged_pull_requests_count":4,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":1,"past_year_pull_requests_count":4,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":3791242.5,"past_year_issues_closed_count":0,"past_year_pull_requests_closed_count":4,"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":0.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":4,"created_at":"2024-11-12T02:26:27.942Z","updated_at":"2025-09-02T18:31:54.567Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Farrakis","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Farrakis/issues","issue_labels_count":{"question":1},"pull_request_labels_count":{},"issue_author_associations_count":{"CONTRIBUTOR":1},"pull_request_author_associations_count":{"MEMBER":6,"NONE":1,"CONTRIBUTOR":1},"issue_authors":{"soccin":1},"pull_request_authors":{"nikhil":6,"soccin":2},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-03T00:00:08.273Z","repositories_count":10060029,"issues_count":31035129,"pull_requests_count":93957968,"authors_count":10685658,"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":{},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{},"past_year_pull_request_author_associations_count":{"MEMBER":2},"past_year_issue_authors":{},"past_year_pull_request_authors":{"nikhil":2},"maintainers":[{"login":"nikhil","count":6,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nikhil"}],"active_maintainers":[{"login":"nikhil","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nikhil"}]},"events":{"total":{"DeleteEvent":1,"PushEvent":9,"PullRequestEvent":3,"CreateEvent":1},"last_year":{"DeleteEvent":1,"PushEvent":9,"PullRequestEvent":3,"CreateEvent":1}},"keywords":[],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:02.317Z","updated_at":"2024-03-05T20:58:02.317Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/.github/workflows/branch.yml","dependencies":[{"id":16627719403,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"b8f338c590a895d50bcbfa6c5859251edc8952fc","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/ci.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:03.422Z","updated_at":"2024-03-05T20:58:03.422Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/.github/workflows/ci.yml","dependencies":[{"id":16627720239,"package_name":"actions/checkout","ecosystem":"actions","requirements":"b4ffde65f46336ab88eb53be808477a3936bae11","direct":true,"kind":"composite","optional":false},{"id":16627720241,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":16627720242,"package_name":"jlumbroso/free-disk-space","ecosystem":"actions","requirements":"54081f138730dfa15788a46383842cd2f914a1be","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/clean-up.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:03.953Z","updated_at":"2024-03-05T20:58:03.953Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/.github/workflows/clean-up.yml","dependencies":[{"id":16627720245,"package_name":"actions/stale","ecosystem":"actions","requirements":"28ca1036281a5e5922ead5184a1bbf96e5fc984e","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/download_pipeline.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:04.226Z","updated_at":"2024-03-05T20:58:04.226Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/.github/workflows/download_pipeline.yml","dependencies":[{"id":16627721018,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":16627721019,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"0a5c61591373683505ea898e09a3ea4f39ef2b9c","direct":true,"kind":"composite","optional":false},{"id":16627721020,"package_name":"eWaterCycle/setup-singularity","ecosystem":"actions","requirements":"931d4e31109e875b13309ae1d07c70ca8fbc8537","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/fix-linting.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:05.658Z","updated_at":"2024-03-05T20:58:05.658Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/.github/workflows/fix-linting.yml","dependencies":[{"id":16627721092,"package_name":"actions/checkout","ecosystem":"actions","requirements":"b4ffde65f46336ab88eb53be808477a3936bae11","direct":true,"kind":"composite","optional":false},{"id":16627721093,"package_name":"peter-evans/create-or-update-comment","ecosystem":"actions","requirements":"71345be0265236311c031f5c7866368bd1eff043","direct":true,"kind":"composite","optional":false},{"id":16627721094,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"0a5c61591373683505ea898e09a3ea4f39ef2b9c","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:05.667Z","updated_at":"2024-03-05T20:58:05.667Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/.github/workflows/linting.yml","dependencies":[{"id":16627721095,"package_name":"actions/checkout","ecosystem":"actions","requirements":"b4ffde65f46336ab88eb53be808477a3936bae11","direct":true,"kind":"composite","optional":false},{"id":16627721096,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"0a5c61591373683505ea898e09a3ea4f39ef2b9c","direct":true,"kind":"composite","optional":false},{"id":16627721097,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":16627721098,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"5d5d22a31266ced268874388b861e4b58bb5c2f3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting_comment.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:05.677Z","updated_at":"2024-03-05T20:58:05.677Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/.github/workflows/linting_comment.yml","dependencies":[{"id":16627721099,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"f6b0bace624032e30a85a8fd9c1a7f8f611f5737","direct":true,"kind":"composite","optional":false},{"id":16627721100,"package_name":"marocchino/sticky-pull-request-comment","ecosystem":"actions","requirements":"331f8f5b4215f0445d3c07b4967662a32a2d3e31","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/release-announcements.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:05.685Z","updated_at":"2024-03-05T20:58:05.685Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/.github/workflows/release-announcements.yml","dependencies":[{"id":16627721101,"package_name":"rzr/fediverse-action","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false},{"id":16627721102,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"0a5c61591373683505ea898e09a3ea4f39ef2b9c","direct":true,"kind":"composite","optional":false},{"id":16627721103,"package_name":"zentered/bluesky-post-action","ecosystem":"actions","requirements":"80dbe0a7697de18c15ad22f4619919ceb5ccf597","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastqc/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:05.969Z","updated_at":"2024-03-05T20:58:05.969Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:05.976Z","updated_at":"2024-03-05T20:58:05.976Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:06.250Z","updated_at":"2024-03-05T20:58:06.250Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nfcore_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:06.427Z","updated_at":"2024-03-05T20:58:06.427Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:06.525Z","updated_at":"2024-03-05T20:58:06.525Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2024-03-05T20:58:07.421Z","updated_at":"2024-03-05T20:58:07.421Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/pyproject.toml","dependencies":[]},{"ecosystem":"conda","filepath":"modules/nf-core/fastqc/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-11T16:06:23.076Z","updated_at":"2024-03-11T16:06:23.076Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/modules/nf-core/fastqc/environment.yml","dependencies":[{"id":16747131817,"package_name":"fastqc","ecosystem":"conda","requirements":"0.12.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/multiqc/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-11T16:06:23.130Z","updated_at":"2024-03-11T16:06:23.130Z","repository_link":"https://github.com/mskcc/arrakis/blob/master/modules/nf-core/multiqc/environment.yml","dependencies":[{"id":16747131835,"package_name":"multiqc","ecosystem":"conda","requirements":"1.21.*","direct":true,"kind":"runtime","optional":false}]}],"score":0.6931471805599453,"created_at":"2025-09-04T15:51:31.515Z","updated_at":"2025-10-07T08:21:59.244Z","avatar_url":"https://github.com/mskcc.png","language":"Nextflow","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.XXXXXXX","https://doi.org/10.1093/bioinformatics/btz033","https://doi.org/10.1002/0471250953.bi1110s43","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/55597","html_url":"https://science.ecosyste.ms/projects/55597","bibtex_url":"https://science.ecosyste.ms/projects/55597/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/55597/export.apalike"}