{"id":43357,"name":"marsseq","description":"MARS-seq v2 pre-processing pipeline with velocity","url":"https://github.com/nf-core/marsseq","last_synced_at":"2025-09-05T09:47:53.500Z","repository":{"id":166758986,"uuid":"387912248","full_name":"nf-core/marsseq","owner":"nf-core","description":"MARS-seq v2 pre-processing pipeline with velocity","archived":false,"fork":false,"pushed_at":"2025-06-02T12:09:18.000Z","size":3545,"stargazers_count":7,"open_issues_count":4,"forks_count":5,"subscribers_count":177,"default_branch":"master","last_synced_at":"2025-06-02T21:31:41.905Z","etag":null,"topics":["facs-sorting","mars-seq","nextflow","nf-core","pipeline","single-cell","single-cell-rna-seq","star-solo","transcriptional-dynamics","workflow"],"latest_commit_sha":null,"homepage":"https://nf-co.re/marsseq","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":"2021-07-20T20:57:04.000Z","updated_at":"2025-06-02T12:15:22.000Z","dependencies_parsed_at":"2024-01-29T16:40:12.482Z","dependency_job_id":"d1a8f88e-4125-4cd0-982a-a03bba780a76","html_url":"https://github.com/nf-core/marsseq","commit_stats":{"total_commits":140,"total_committers":5,"mean_commits":28.0,"dds":0.5142857142857142,"last_synced_commit":"b02ede773092f8a8a5999400acda6894d51b4d26"},"previous_names":["matq007/nf-core-marsseq","nf-core/marsseq"],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/nf-core/marsseq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmarsseq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmarsseq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmarsseq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmarsseq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core","download_url":"https://codeload.github.com/nf-core/marsseq/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmarsseq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273740677,"owners_count":25159433,"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":1317676,"full_name":"nf-core/marsseq","default_branch":"master","committers":[{"name":"Martin Proks","email":"mproksik@gmail.com","login":null,"count":68},{"name":"Martin Proks","email":"martin.proks@sund.ku.dk","login":null,"count":48},{"name":"fdb589","email":"fdb589@dangpu01fl.unicph.domain","login":null,"count":18},{"name":"Maxime U Garcia","email":"maxime.garcia@seqera.io","login":null,"count":5},{"name":"nf-core-bot","email":"core@nf-co.re","login":null,"count":1}],"total_commits":140,"total_committers":5,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":28.0,"dds":0.5142857142857142,"past_year_committers":[{"name":"Martin Proks","email":"martin.proks@sund.ku.dk","login":null,"count":48},{"name":"Maxime U Garcia","email":"maxime.garcia@seqera.io","login":null,"count":5},{"name":"Martin","email":"mproksik@gmail.com","login":null,"count":3},{"name":"nf-core-bot","email":"core@nf-co.re","login":null,"count":1}],"past_year_total_commits":57,"past_year_total_committers":4,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":14.25,"past_year_dds":0.1578947368421053,"last_synced_at":"2023-11-04T18:31:23.581Z","last_synced_commit":"b02ede773092f8a8a5999400acda6894d51b4d26","created_at":"2023-06-15T18:11:43.943Z","updated_at":"2023-11-04T18:31:23.582Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmarsseq/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":"nf-core/marsseq","html_url":"https://github.com/nf-core/marsseq","last_synced_at":"2025-08-31T14:00:10.514Z","status":null,"issues_count":9,"pull_requests_count":10,"avg_time_to_close_issue":630939.0,"avg_time_to_close_pull_request":1400198.875,"issues_closed_count":3,"pull_requests_closed_count":8,"pull_request_authors_count":3,"issue_authors_count":6,"avg_comments_per_issue":0.7777777777777778,"avg_comments_per_pull_request":1.4,"merged_pull_requests_count":6,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":5,"past_year_pull_requests_count":3,"past_year_avg_time_to_close_issue":149817.0,"past_year_avg_time_to_close_pull_request":4316141.5,"past_year_issues_closed_count":1,"past_year_pull_requests_closed_count":2,"past_year_pull_request_authors_count":1,"past_year_issue_authors_count":4,"past_year_avg_comments_per_issue":0.4,"past_year_avg_comments_per_pull_request":0.6666666666666666,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":0,"created_at":"2023-06-15T18:11:52.612Z","updated_at":"2025-09-03T04:58:16.678Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmarsseq","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmarsseq/issues","issue_labels_count":{"bug":5,"enhancement":2,"documentation":1},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":9,"MEMBER":2},"pull_request_author_associations_count":{"MEMBER":21},"issue_authors":{"matq007":2,"dslarm":2,"UboCA":2,"famosab":1,"nvnieuwk":1,"lindenb":1,"jen-reeve":1,"huawen-poppy":1},"pull_request_authors":{"nf-core-bot":16,"matq007":4,"maxulysse":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10095847,"issues_count":31414178,"pull_requests_count":97181322,"authors_count":10701051,"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":{"NONE":5},"past_year_pull_request_author_associations_count":{"MEMBER":9},"past_year_issue_authors":{"dslarm":2,"famosab":1,"jen-reeve":1,"lindenb":1},"past_year_pull_request_authors":{"nf-core-bot":8,"matq007":1},"maintainers":[{"login":"nf-core-bot","count":16,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"matq007","count":6,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/matq007"},{"login":"maxulysse","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/maxulysse"}],"active_maintainers":[{"login":"nf-core-bot","count":8,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"matq007","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/matq007"}]},"events":{"total":{"IssuesEvent":9,"WatchEvent":3,"IssueCommentEvent":10,"PushEvent":26,"PullRequestReviewEvent":9,"PullRequestReviewCommentEvent":7,"PullRequestEvent":12,"CreateEvent":6},"last_year":{"IssuesEvent":9,"WatchEvent":3,"IssueCommentEvent":10,"PushEvent":26,"PullRequestReviewEvent":9,"PullRequestReviewCommentEvent":7,"PullRequestEvent":12,"CreateEvent":6}},"keywords":["facs-sorting","mars-seq","nextflow","nf-core","pipeline","single-cell","single-cell-rna-seq","star-solo","transcriptional-dynamics","workflow"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/awsfulltest.yml","sha":null,"kind":"manifest","created_at":"2023-06-01T08:46:29.319Z","updated_at":"2023-06-01T08:46:29.319Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/.github/workflows/awsfulltest.yml","dependencies":[{"id":10239654458,"package_name":"nf-core/tower-action","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/awstest.yml","sha":null,"kind":"manifest","created_at":"2023-06-01T08:46:29.555Z","updated_at":"2023-06-01T08:46:29.555Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/.github/workflows/awstest.yml","dependencies":[{"id":10239654508,"package_name":"nf-core/tower-action","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2023-06-01T08:46:29.650Z","updated_at":"2023-06-01T08:46:29.650Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/.github/workflows/branch.yml","dependencies":[{"id":10239654773,"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":"2023-06-01T08:46:29.711Z","updated_at":"2023-06-01T08:46:29.711Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/.github/workflows/ci.yml","dependencies":[{"id":10239654832,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting.yml","sha":null,"kind":"manifest","created_at":"2023-06-01T08:46:29.776Z","updated_at":"2023-06-01T08:46:29.776Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/.github/workflows/linting.yml","dependencies":[{"id":10239654889,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":10239654890,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":10239654891,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":10239654892,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":10239654893,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":10239654894,"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":"2023-06-01T08:46:29.879Z","updated_at":"2023-06-01T08:46:29.879Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/.github/workflows/linting_comment.yml","dependencies":[{"id":10239655587,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":10239655590,"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":"2023-09-23T11:12:47.073Z","updated_at":"2023-09-23T11:12:47.073Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/.github/workflows/clean-up.yml","dependencies":[{"id":13897709892,"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":"2023-09-23T11:12:47.123Z","updated_at":"2023-09-23T11:12:47.123Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/.github/workflows/fix-linting.yml","dependencies":[{"id":13897709906,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":13897709907,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/local/ercc/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:09.331Z","updated_at":"2024-01-29T16:40:09.331Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/local/ercc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/local/fastp/split/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:09.438Z","updated_at":"2024-01-29T16:40:09.438Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/local/fastp/split/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/local/wget/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:09.445Z","updated_at":"2024-01-29T16:40:09.445Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/local/wget/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/bowtie2/align/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:09.954Z","updated_at":"2024-01-29T16:40:09.954Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/nf-core/bowtie2/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/bowtie2/build/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:10.211Z","updated_at":"2024-01-29T16:40:10.211Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/nf-core/bowtie2/build/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/cat/cat/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:10.614Z","updated_at":"2024-01-29T16:40:10.614Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/nf-core/cat/cat/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/custom/dumpsoftwareversions/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:10.642Z","updated_at":"2024-01-29T16:40:10.642Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/nf-core/custom/dumpsoftwareversions/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/cutadapt/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:10.963Z","updated_at":"2024-01-29T16:40:10.963Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/nf-core/cutadapt/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastqc/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:10.984Z","updated_at":"2024-01-29T16:40:10.984Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/gunzip/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:11.299Z","updated_at":"2024-01-29T16:40:11.299Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/nf-core/gunzip/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:11.545Z","updated_at":"2024-01-29T16:40:11.545Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/star/align/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:11.884Z","updated_at":"2024-01-29T16:40:11.884Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/nf-core/star/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/star/genomegenerate/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:12.172Z","updated_at":"2024-01-29T16:40:12.172Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/modules/nf-core/star/genomegenerate/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2024-01-29T16:40:12.193Z","updated_at":"2024-01-29T16:40:12.193Z","repository_link":"https://github.com/nf-core/marsseq/blob/master/pyproject.toml","dependencies":[]}],"score":4.007333185232471,"created_at":"2025-09-04T15:51:18.401Z","updated_at":"2025-10-07T08:17:34.258Z","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.8063539","https://doi.org/10.1038/s41596-019-0164-4","https://dx.doi.org/10.1038/s41587-020-0439-x"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["pipelines","workflows","bioinformatics"],"project_url":"https://science.ecosyste.ms/api/v1/projects/43357","html_url":"https://science.ecosyste.ms/projects/43357","bibtex_url":"https://science.ecosyste.ms/projects/43357/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/43357/export.apalike"}