{"id":43103,"name":"scrnaseq","description":"Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection","url":"https://github.com/nf-core/scrnaseq","last_synced_at":"2025-09-05T09:42:40.370Z","repository":{"id":37090297,"uuid":"180151993","full_name":"nf-core/scrnaseq","owner":"nf-core","description":"Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection","archived":false,"fork":false,"pushed_at":"2025-08-01T10:32:27.000Z","size":45796,"stargazers_count":285,"open_issues_count":72,"forks_count":194,"subscribers_count":152,"default_branch":"master","last_synced_at":"2025-08-01T10:39:46.825Z","etag":null,"topics":["10x-genomics","10xgenomics","alevin","bustools","cellranger","kallisto","nextflow","nf-core","pipeline","rna-seq","single-cell","star-solo","workflow"],"latest_commit_sha":null,"homepage":"https://nf-co.re/scrnaseq","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/nf-core.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":"2019-04-08T13:12:00.000Z","updated_at":"2025-07-30T05:01:14.000Z","dependencies_parsed_at":"2023-09-23T00:14:07.313Z","dependency_job_id":"be834d67-7a61-4b96-99e6-c2985b2169b5","html_url":"https://github.com/nf-core/scrnaseq","commit_stats":{"total_commits":785,"total_committers":41,"mean_commits":"19.146341463414632","dds":0.7630573248407644,"last_synced_commit":"ca7c05afdd5c41dc31a5a32bb207d19767836ca5"},"previous_names":[],"tags_count":17,"template":false,"template_full_name":null,"purl":"pkg:github/nf-core/scrnaseq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscrnaseq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscrnaseq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscrnaseq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscrnaseq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core","download_url":"https://codeload.github.com/nf-core/scrnaseq/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscrnaseq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273740043,"owners_count":25159429,"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":"nf-core","name":"nf-core","uuid":"35520196","kind":"organization","description":"A community effort to collect a curated set of analysis pipelines built using Nextflow.","email":"core@nf-co.re","website":"http://nf-co.re","location":null,"twitter":"nf_core","company":null,"icon_url":"https://avatars.githubusercontent.com/u/35520196?v=4","repositories_count":84,"last_synced_at":"2023-03-01T20:50:19.252Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/nf-core","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-12T16:29:01.932Z","updated_at":"2023-03-01T20:50:19.281Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core/repositories"},"packages":[],"commits":{"id":1317656,"full_name":"nf-core/scrnaseq","default_branch":"master","committers":[{"name":"Alexander Peltzer","email":"alex.peltzer@gmail.com","login":null,"count":186},{"name":"Felipe Marques de Almeida","email":"almeidafmarques@gmail.com","login":null,"count":107},{"name":"Olga Botvinnik","email":"olga.botvinnik@gmail.com","login":null,"count":61},{"name":"Gregor Sturm","email":"mail@gregor-sturm.de","login":null,"count":37},{"name":"Felipe Marques de Almeida","email":"felipemarques89@gmail.com","login":null,"count":33},{"name":"kevinmenden","email":"kevin.menden@t-online.de","login":null,"count":31},{"name":"nf-core-bot","email":"core@nf-co.re","login":null,"count":31},{"name":"Alexander Peltzer","email":"apeltzer","login":"apeltzer","count":26},{"name":"Gregor Sturm","email":"gregor.sturm@boehringer-ingelheim.com","login":null,"count":26},{"name":"Alexander Peltzer","email":"alexander.peltzer@boehringer-ingelheim.com","login":null,"count":25},{"name":"Sangram Keshari Sahu","email":"sangramsahu15@gmail.com","login":null,"count":22},{"name":"Pol Alvarez","email":"pol.avms@gmail.com","login":null,"count":21},{"name":"Rob Syme","email":"rob.syme@gmail.com","login":null,"count":19},{"name":"Adam Talbot","email":"adam.talbot@seqera.io","login":null,"count":18},{"name":"ggabernet","email":"gisela.gabernet@qbic.uni-tuebingen.de","login":null,"count":16},{"name":"Florian","email":"flo.minion.info@gmail.com","login":null,"count":15},{"name":"Alison Meynert","email":"ameyner2@ed.ac.uk","login":null,"count":15},{"name":"TomKellyGenetics","email":"tomkellygenetics@gmail.com","login":null,"count":14},{"name":"Harshil Patel","email":"drpatelhh@gmail.com","login":null,"count":12},{"name":"maxulysse","email":"max.u.garcia@gmail.com","login":null,"count":10},{"name":"PeterBailey","email":"Peter.Bailey.2@glasgow.ac.uk","login":null,"count":10},{"name":"Alex Thiery","email":"alexandre.thiery@kcl.ac.uk","login":null,"count":7},{"name":"Harshil Patel","email":"drpatelh","login":"drpatelh","count":5},{"name":"Azedine Zoufir","email":"41290849+azedine-healx","login":"azedine-healx","count":5},{"name":"Hana Medova","email":"53634881+medulka","login":"medulka","count":5},{"name":"RHReynolds","email":"regina.reynolds.16@ucl.ac.uk","login":null,"count":5},{"name":"Khajidu","email":"Khajidu","login":"Khajidu","count":4},{"name":"Adam Talbot","email":"12817534+adamrtalbot","login":"adamrtalbot","count":3},{"name":"Marcel Ribeiro-Dantas","email":"marcel.ribeiro-dantas@curie.fr","login":null,"count":2},{"name":"Gisela Gabernet","email":"gisela.gabernet@gmail.com","login":null,"count":2},{"name":"Wei-An Chen","email":"boochachawc@gmail.com","login":null,"count":2},{"name":"runner","email":"runner@fv-az60","login":null,"count":1},{"name":"vjmarteau","email":"valentinmarteau7@gmail.com","login":null,"count":1},{"name":"Stan Werbrouck","email":"stan.werbrouck@student.howest.be","login":null,"count":1},{"name":"shinthor","email":"44301097+shinthor","login":"shinthor","count":1},{"name":"Maxime U Garcia","email":"maxime.garcia@seqera.io","login":null,"count":1},{"name":"Peter Bailey","email":"peterbailey@peters-mbp.home","login":null,"count":1},{"name":"Sangram K Sahu","email":"sangram@lifebit.ai","login":null,"count":1},{"name":"EC2 Default User","email":"ec2-user@ip-172-31-11-186.ec2.internal","login":null,"count":1},{"name":"Jeremy Leipzig","email":"leipzig@gmail.com","login":null,"count":1},{"name":"peterbailey","email":"peterbailey@Peters-MBP","login":null,"count":1}],"total_commits":785,"total_committers":41,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":19.146341463414632,"dds":0.7630573248407644,"past_year_committers":[{"name":"Alexander Peltzer","email":"alex.peltzer@gmail.com","login":null,"count":42},{"name":"Gregor Sturm","email":"gregor.sturm@boehringer-ingelheim.com","login":null,"count":26},{"name":"Pol Alvarez","email":"pol.avms@gmail.com","login":null,"count":21},{"name":"Adam Talbot","email":"adam.talbot@seqera.io","login":null,"count":18},{"name":"Alison Meynert","email":"ameyner2@ed.ac.uk","login":null,"count":15},{"name":"TomKellyGenetics","email":"tomkellygenetics@gmail.com","login":null,"count":14},{"name":"nf-core-bot","email":"core@nf-co.re","login":null,"count":10},{"name":"Felipe Marques de Almeida","email":"felipemarques89@gmail.com","login":null,"count":10},{"name":"Harshil Patel","email":"drpatelhh@gmail.com","login":null,"count":9},{"name":"Florian","email":"flo.minion.info@gmail.com","login":null,"count":9},{"name":"maxulysse","email":"max.u.garcia@gmail.com","login":null,"count":8},{"name":"Gregor Sturm","email":"mail@gregor-sturm.de","login":null,"count":8},{"name":"Rob Syme","email":"rob.syme@gmail.com","login":null,"count":5},{"name":"Azedine Zoufir","email":"41290849+azedine-healx","login":"azedine-healx","count":5},{"name":"Adam Talbot","email":"12817534+adamrtalbot","login":"adamrtalbot","count":3},{"name":"Wei-An Chen","email":"boochachawc@gmail.com","login":null,"count":2},{"name":"Alexander Peltzer","email":"apeltzer","login":"apeltzer","count":2},{"name":"Harshil Patel","email":"drpatelh","login":"drpatelh","count":2},{"name":"Stan Werbrouck","email":"stan.werbrouck@student.howest.be","login":null,"count":1},{"name":"shinthor","email":"44301097+shinthor","login":"shinthor","count":1},{"name":"Maxime U Garcia","email":"maxime.garcia@seqera.io","login":null,"count":1}],"past_year_total_commits":212,"past_year_total_committers":21,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":10.095238095238095,"past_year_dds":0.8018867924528301,"last_synced_at":"2023-11-04T18:32:29.034Z","last_synced_commit":"ca7c05afdd5c41dc31a5a32bb207d19767836ca5","created_at":"2023-06-15T18:09:19.550Z","updated_at":"2023-11-04T18:32:29.035Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscrnaseq/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-08-27T00:00:29.048Z","repositories_count":5479765,"commits_count":853308191,"contributors_count":31095157,"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":"nf-core/scrnaseq","html_url":"https://github.com/nf-core/scrnaseq","last_synced_at":"2025-08-31T09:02:08.849Z","status":null,"issues_count":106,"pull_requests_count":132,"avg_time_to_close_issue":13153425.924242424,"avg_time_to_close_pull_request":1363426.7413793104,"issues_closed_count":66,"pull_requests_closed_count":116,"pull_request_authors_count":36,"issue_authors_count":69,"avg_comments_per_issue":3.481132075471698,"avg_comments_per_pull_request":2.7803030303030303,"merged_pull_requests_count":99,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":25,"past_year_pull_requests_count":41,"past_year_avg_time_to_close_issue":4275703.363636363,"past_year_avg_time_to_close_pull_request":432925.14285714284,"past_year_issues_closed_count":11,"past_year_pull_requests_closed_count":28,"past_year_pull_request_authors_count":18,"past_year_issue_authors_count":20,"past_year_avg_comments_per_issue":1.28,"past_year_avg_comments_per_pull_request":1.829268292682927,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":26,"created_at":"2023-05-16T03:44:18.764Z","updated_at":"2025-09-03T06:52:09.841Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscrnaseq","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fscrnaseq/issues","issue_labels_count":{"bug":74,"enhancement":68,"quality \u0026 consistency":7,"good first issue":2,"help wanted":2,"question":1,"documentation":1,"alevin":1,"cellranger-arc":1,"bug-confirmed":1},"pull_request_labels_count":{"Ready for review":9,"enhancement":8,"bug":5,"DO_NOT_MERGE":2},"issue_author_associations_count":{"NONE":97,"MEMBER":32,"CONTRIBUTOR":26},"pull_request_author_associations_count":{"MEMBER":91,"CONTRIBUTOR":71,"NONE":30},"issue_authors":{"grst":21,"nick-youngblut":14,"fmalmeida":5,"tomsing1":4,"wzheng0520":4,"svigneau":3,"Vivian-chen16":3,"rhodesch":3,"adamrtalbot":3,"alexblaessle":3,"apeltzer":3,"asp8200":2,"heylf":2,"maggiebr0wn":2,"Khajidu":2,"ChristopherMancuso":2,"ChristopherBarrington":2,"FelixKrueger":2,"RoganGrant":2,"pinin4fjords":2,"ashwinikumarkulkarni":2,"sean-at-tessera":1,"marcus-tutert":1,"saraterzo":1,"BurtonChia":1,"irenemaring":1,"ogibson":1,"sclan":1,"sajjadasaf":1,"berguner":1,"Xhepone":1,"esrice":1,"ohsumit":1,"ninamurrell":1,"TomKellyGenetics":1,"suhrig":1,"jeremymsimon":1,"Yaxiong293":1,"Zethson":1,"mossjacob":1,"Juassis":1,"ffmmulder":1,"ameynert":1,"asmaali98":1,"stevekm":1,"loguille":1,"winni2k":1,"JosephAgim":1,"nictru":1,"esamorodnitsky":1,"adairama":1,"jjovelc":1,"KeLi1018":1,"melissamlwong18":1,"matq007":1,"jiehuichen":1,"jhgraber":1,"mikecuoco":1,"Mridul-Chaudhary":1,"SaraTerzol":1,"pablasimarjot":1,"ggabernet":1,"DongzeHE":1,"olgabot":1,"Zhenghongc":1,"denisthieffry":1,"ozill12":1,"galanisl":1,"lewis9914":1,"zeehio":1,"martinkim0":1,"vjmarteau":1,"RPSeaman":1,"pakiessling":1,"davidecarlson":1,"SarahBeecroft":1,"fbnrst":1,"MaestSi":1,"zvittorio":1,"zhewa":1,"klkeys":1,"mschubert":1,"SethMagnusJarvis":1,"davhum":1,"kafkasl":1,"LizEve":1,"divyanshusrivastava":1,"wblashka":1,"lfperales":1,"birgitritschka":1},"pull_request_authors":{"grst":50,"fmalmeida":29,"nf-core-bot":20,"apeltzer":10,"heylf":9,"adamrtalbot":8,"nictru":7,"kafkasl":5,"robsyme":5,"drpatelh":4,"DongzeHE":3,"wzheng0520":2,"Vivian-chen16":2,"kopichris":2,"nick-youngblut":2,"ameynert":2,"herpov":2,"milos7250":2,"matq007":2,"Khajidu":2,"esrice":1,"lazappi":1,"haibol2016":1,"maxulysse":1,"stan0610":1,"chris-cheshire":1,"matbonfanti":1,"saraterzo":1,"abyssum":1,"svigneau":1,"TomKellyGenetics":1,"sandrocarollo":1,"Mridul-Chaudhary":1,"shinthor":1,"FelixKrueger":1,"eolaniru":1,"azedine-healx":1,"LeonHafner":1,"abartlett004":1,"gennadyFauna":1,"rlinchangco":1,"an-altosian":1,"corey-hayford":1,"shenkers":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10095926,"issues_count":31397479,"pull_requests_count":97150418,"authors_count":10700329,"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":22,"enhancement":14,"alevin":1,"quality \u0026 consistency":1,"cellranger-arc":1},"past_year_pull_request_labels_count":{"enhancement":3,"bug":2},"past_year_issue_author_associations_count":{"NONE":28,"CONTRIBUTOR":9,"MEMBER":4},"past_year_pull_request_author_associations_count":{"CONTRIBUTOR":25,"MEMBER":19,"NONE":16},"past_year_issue_authors":{"nick-youngblut":7,"grst":3,"svigneau":3,"ChristopherBarrington":2,"wzheng0520":2,"fmalmeida":2,"Zhenghongc":1,"Yaxiong293":1,"Xhepone":1,"SaraTerzol":1,"saraterzo":1,"sajjadasaf":1,"RoganGrant":1,"ohsumit":1,"ninamurrell":1,"Mridul-Chaudhary":1,"mossjacob":1,"melissamlwong18":1,"marcus-tutert":1,"maggiebr0wn":1,"LizEve":1,"JosephAgim":1,"jiehuichen":1,"irenemaring":1,"fbnrst":1,"esrice":1,"esamorodnitsky":1,"davhum":1},"past_year_pull_request_authors":{"fmalmeida":17,"nf-core-bot":7,"nictru":6,"grst":4,"apeltzer":3,"wzheng0520":2,"DongzeHE":2,"matq007":2,"kopichris":2,"milos7250":2,"FelixKrueger":1,"svigneau":1,"saraterzo":1,"matbonfanti":1,"nick-youngblut":1,"lazappi":1,"haibol2016":1,"an-altosian":1,"esrice":1,"shenkers":1,"LeonHafner":1,"Mridul-Chaudhary":1,"abartlett004":1},"maintainers":[{"login":"grst","count":71,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/grst"},{"login":"nf-core-bot","count":20,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"apeltzer","count":13,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/apeltzer"},{"login":"drpatelh","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/drpatelh"},{"login":"matq007","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/matq007"},{"login":"pinin4fjords","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/pinin4fjords"},{"login":"RoganGrant","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/RoganGrant"},{"login":"DongzeHE","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/DongzeHE"},{"login":"TomKellyGenetics","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/TomKellyGenetics"},{"login":"ggabernet","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/ggabernet"},{"login":"lazappi","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/lazappi"},{"login":"Zethson","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/Zethson"},{"login":"maxulysse","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/maxulysse"}],"active_maintainers":[{"login":"nf-core-bot","count":7,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"grst","count":7,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/grst"},{"login":"apeltzer","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/apeltzer"},{"login":"DongzeHE","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/DongzeHE"},{"login":"matq007","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/matq007"},{"login":"RoganGrant","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/RoganGrant"},{"login":"lazappi","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/lazappi"}]},"events":{"total":{"CreateEvent":35,"ReleaseEvent":1,"IssuesEvent":65,"WatchEvent":72,"DeleteEvent":37,"MemberEvent":1,"IssueCommentEvent":313,"PushEvent":175,"PullRequestEvent":97,"PullRequestReviewEvent":161,"PullRequestReviewCommentEvent":143,"ForkEvent":38},"last_year":{"CreateEvent":35,"ReleaseEvent":1,"IssuesEvent":65,"WatchEvent":72,"DeleteEvent":37,"MemberEvent":1,"IssueCommentEvent":313,"PushEvent":175,"PullRequestEvent":97,"PullRequestReviewEvent":161,"PullRequestReviewCommentEvent":143,"ForkEvent":38}},"keywords":["10x-genomics","10xgenomics","alevin","bustools","cellranger","kallisto","nextflow","nf-core","pipeline","rna-seq","single-cell","star-solo","workflow"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/awsfulltest.yml","sha":null,"kind":"manifest","created_at":"2023-01-29T22:15:14.053Z","updated_at":"2023-01-29T22:15:14.053Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/.github/workflows/awsfulltest.yml","dependencies":[{"id":7232945432,"package_name":"nf-core/tower-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7232945433,"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":"2023-01-29T22:15:14.390Z","updated_at":"2023-01-29T22:15:14.390Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/.github/workflows/awstest.yml","dependencies":[{"id":7232947830,"package_name":"nf-core/tower-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7232947831,"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":"2023-01-29T22:15:14.878Z","updated_at":"2023-01-29T22:15:14.878Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/.github/workflows/branch.yml","dependencies":[{"id":7232948191,"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":"2023-01-29T22:15:15.105Z","updated_at":"2023-01-29T22:15:15.105Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/.github/workflows/ci.yml","dependencies":[{"id":7232949392,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7232949393,"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":"2023-01-29T22:15:15.404Z","updated_at":"2023-01-29T22:15:15.404Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/.github/workflows/fix-linting.yml","dependencies":[{"id":7232949861,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7232949864,"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":"2023-01-29T22:15:15.795Z","updated_at":"2023-01-29T22:15:15.795Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/.github/workflows/linting.yml","dependencies":[{"id":7232954042,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7232954043,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7232954044,"package_name":"psf/black","ecosystem":"actions","requirements":"stable","direct":true,"kind":"composite","optional":false},{"id":7232954045,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7232954046,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7232954047,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":7232954048,"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":"2023-01-29T22:15:15.922Z","updated_at":"2023-01-29T22:15:15.922Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/.github/workflows/linting_comment.yml","dependencies":[{"id":7232954717,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7232954718,"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":"2023-09-23T00:14:04.203Z","updated_at":"2023-09-23T00:14:04.203Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/.github/workflows/clean-up.yml","dependencies":[{"id":13886076732,"package_name":"actions/stale","ecosystem":"actions","requirements":"v7","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/cellranger/count/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:04.530Z","updated_at":"2023-09-23T00:14:04.530Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/cellranger/count/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/cellranger/mkgtf/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:04.596Z","updated_at":"2023-09-23T00:14:04.596Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/cellranger/mkgtf/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/cellranger/mkref/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:04.647Z","updated_at":"2023-09-23T00:14:04.647Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/cellranger/mkref/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/custom/dumpsoftwareversions/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:04.737Z","updated_at":"2023-09-23T00:14:04.737Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/custom/dumpsoftwareversions/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastqc/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:04.880Z","updated_at":"2023-09-23T00:14:04.880Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/gffread/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:04.960Z","updated_at":"2023-09-23T00:14:04.960Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/gffread/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/gunzip/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:05.039Z","updated_at":"2023-09-23T00:14:05.039Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/gunzip/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/kallistobustools/count/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:05.173Z","updated_at":"2023-09-23T00:14:05.173Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/kallistobustools/count/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/kallistobustools/ref/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:05.273Z","updated_at":"2023-09-23T00:14:05.273Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/kallistobustools/ref/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:05.674Z","updated_at":"2023-09-23T00:14:05.674Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/star/genomegenerate/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:05.770Z","updated_at":"2023-09-23T00:14:05.770Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/star/genomegenerate/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/universc/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:05.880Z","updated_at":"2023-09-23T00:14:05.880Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/modules/nf-core/universc/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2023-09-23T00:14:06.734Z","updated_at":"2023-09-23T00:14:06.734Z","repository_link":"https://github.com/nf-core/scrnaseq/blob/master/pyproject.toml","dependencies":[]}],"score":9.591307848483947,"created_at":"2025-09-04T15:51:18.102Z","updated_at":"2025-10-07T08:17:29.315Z","avatar_url":"https://github.com/nf-core.png","language":"Nextflow","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.3568187"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["workflows","metagenomics","pipelines","bioinformatics","nf-test","dsl2","illumina","taxonomic-classification","taxonomic-profiling","airr"],"project_url":"https://science.ecosyste.ms/api/v1/projects/43103","html_url":"https://science.ecosyste.ms/projects/43103","bibtex_url":"https://science.ecosyste.ms/projects/43103/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/43103/export.apalike"}