{"id":43575,"name":"pangenome","description":"Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.","url":"https://github.com/nf-core/pangenome","last_synced_at":"2025-09-05T09:53:07.897Z","repository":{"id":40294613,"uuid":"311123048","full_name":"nf-core/pangenome","owner":"nf-core","description":"Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.","archived":false,"fork":false,"pushed_at":"2025-07-08T11:38:36.000Z","size":4486,"stargazers_count":91,"open_issues_count":15,"forks_count":20,"subscribers_count":80,"default_branch":"master","last_synced_at":"2025-07-08T12:44:37.044Z","etag":null,"topics":["nextflow","nf-core","pangenome","pipeline","workflow"],"latest_commit_sha":null,"homepage":"https://nf-co.re/pangenome","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"subwaystation/pangenome","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":"2020-11-08T18:02:43.000Z","updated_at":"2025-06-30T03:14:01.000Z","dependencies_parsed_at":"2024-03-14T11:42:35.789Z","dependency_job_id":"4c1995f5-958c-45f3-a81c-db0a4be54a69","html_url":"https://github.com/nf-core/pangenome","commit_stats":{"total_commits":427,"total_committers":8,"mean_commits":53.375,"dds":0.1241217798594848,"last_synced_commit":"fc6afebc8ff72f7f95a860e39e1bbb0a88817c06"},"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/nf-core/pangenome","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fpangenome","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fpangenome/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fpangenome/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fpangenome/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core","download_url":"https://codeload.github.com/nf-core/pangenome/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fpangenome/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273740855,"owners_count":25159434,"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":1317650,"full_name":"nf-core/pangenome","default_branch":"master","committers":[{"name":"subwaystation","email":"simon.heumos@qbic.uni-tuebingen.de","login":null,"count":374},{"name":"nf-core-bot","email":"core@nf-co.re","login":null,"count":21},{"name":"AndreaGuarracino","email":"andreaguarracino@outlook.com","login":null,"count":12},{"name":"Lukas Heumos","email":"lukas.heumos@posteo.net","login":null,"count":10},{"name":"Michael L Heuer","email":"heuermh@acm.org","login":null,"count":6},{"name":"Lukas Heumos","email":"lukas.heumos@gmail.com","login":null,"count":2},{"name":"James A. Fellows Yates","email":"jfy133@gmail.com","login":null,"count":1},{"name":"kevinmenden","email":"kevin.menden@t-online.de","login":null,"count":1}],"total_commits":427,"total_committers":8,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":53.375,"dds":0.1241217798594848,"past_year_committers":[{"name":"subwaystation","email":"simon.heumos@qbic.uni-tuebingen.de","login":null,"count":283},{"name":"nf-core-bot","email":"core@nf-co.re","login":null,"count":7},{"name":"James A. Fellows Yates","email":"jfy133@gmail.com","login":null,"count":1}],"past_year_total_commits":291,"past_year_total_committers":3,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":97.0,"past_year_dds":0.027491408934707917,"last_synced_at":"2023-11-04T18:33:02.351Z","last_synced_commit":"fc6afebc8ff72f7f95a860e39e1bbb0a88817c06","created_at":"2023-06-15T18:09:18.711Z","updated_at":"2023-11-04T18:33:02.352Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fpangenome/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/pangenome","html_url":"https://github.com/nf-core/pangenome","last_synced_at":"2025-08-31T09:16:45.622Z","status":null,"issues_count":54,"pull_requests_count":118,"avg_time_to_close_issue":16993196.51162791,"avg_time_to_close_pull_request":1016565.9292035399,"issues_closed_count":43,"pull_requests_closed_count":113,"pull_request_authors_count":9,"issue_authors_count":13,"avg_comments_per_issue":1.9074074074074074,"avg_comments_per_pull_request":1.533898305084746,"merged_pull_requests_count":84,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":9,"past_year_pull_requests_count":27,"past_year_avg_time_to_close_issue":603540.6666666666,"past_year_avg_time_to_close_pull_request":220096.81818181818,"past_year_issues_closed_count":6,"past_year_pull_requests_closed_count":22,"past_year_pull_request_authors_count":4,"past_year_issue_authors_count":5,"past_year_avg_comments_per_issue":1.5555555555555556,"past_year_avg_comments_per_pull_request":1.8888888888888888,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":17,"created_at":"2023-06-15T18:09:57.062Z","updated_at":"2025-09-03T04:58:16.674Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fpangenome","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fpangenome/issues","issue_labels_count":{"enhancement":42,"bug":13,"documentation":1,"help wanted":1,"question":1,"chore":1,"advanced":1},"pull_request_labels_count":{},"issue_author_associations_count":{"COLLABORATOR":36,"NONE":14,"CONTRIBUTOR":7,"MEMBER":3},"pull_request_author_associations_count":{"COLLABORATOR":100,"MEMBER":33,"CONTRIBUTOR":17,"NONE":3},"issue_authors":{"subwaystation":36,"heuermh":7,"mictadlo":5,"OZTaekOppa":1,"DPI-NZ":1,"nvnieuwk":1,"msgr0":1,"dbrami":1,"maxulysse":1,"JWDebler":1,"SarahBeecroft":1,"jen-reeve":1,"chenhijy":1,"apeltzer":1,"Zethson":1},"pull_request_authors":{"subwaystation":100,"nf-core-bot":31,"heuermh":13,"AndreaGuarracino":2,"KevinMenden":2,"adamrtalbot":1,"ewels":1,"Zethson":1,"nvnieuwk":1,"heringerp":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-04T00:00:25.939Z","repositories_count":10076078,"issues_count":31296153,"pull_requests_count":95886442,"authors_count":10691401,"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":4,"bug":4,"help wanted":1},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"NONE":4,"COLLABORATOR":3,"CONTRIBUTOR":3},"past_year_pull_request_author_associations_count":{"CONTRIBUTOR":13,"COLLABORATOR":9,"MEMBER":8,"NONE":1},"past_year_issue_authors":{"heuermh":3,"subwaystation":3,"chenhijy":1,"jen-reeve":1,"JWDebler":1,"msgr0":1},"past_year_pull_request_authors":{"heuermh":13,"subwaystation":9,"nf-core-bot":8,"nvnieuwk":1},"maintainers":[{"login":"subwaystation","count":136,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/subwaystation"},{"login":"nf-core-bot","count":31,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"Zethson","count":2,"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"},{"login":"apeltzer","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/apeltzer"},{"login":"ewels","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/ewels"}],"active_maintainers":[{"login":"subwaystation","count":12,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/subwaystation"},{"login":"nf-core-bot","count":8,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"}]},"events":{"total":{"CreateEvent":13,"ReleaseEvent":1,"IssuesEvent":18,"WatchEvent":23,"DeleteEvent":3,"IssueCommentEvent":94,"PushEvent":28,"PullRequestReviewCommentEvent":22,"PullRequestReviewEvent":31,"PullRequestEvent":56,"ForkEvent":3},"last_year":{"CreateEvent":13,"ReleaseEvent":1,"IssuesEvent":18,"WatchEvent":23,"DeleteEvent":3,"IssueCommentEvent":94,"PushEvent":28,"PullRequestReviewCommentEvent":22,"PullRequestReviewEvent":31,"PullRequestEvent":56,"ForkEvent":3}},"keywords":["nextflow","nf-core","pangenome","pipeline","workflow"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/awsfulltest.yml","sha":null,"kind":"manifest","created_at":"2023-02-13T19:31:48.927Z","updated_at":"2023-02-13T19:31:48.927Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/.github/workflows/awsfulltest.yml","dependencies":[{"id":7628873808,"package_name":"conda-incubator/setup-miniconda","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/awstest.yml","sha":null,"kind":"manifest","created_at":"2023-02-13T19:31:49.401Z","updated_at":"2023-02-13T19:31:49.401Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/.github/workflows/awstest.yml","dependencies":[{"id":7628878616,"package_name":"conda-incubator/setup-miniconda","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2023-02-13T19:31:49.625Z","updated_at":"2023-02-13T19:31:49.625Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/.github/workflows/branch.yml","dependencies":[{"id":7628879084,"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":"2023-02-13T19:31:49.899Z","updated_at":"2023-02-13T19:31:49.899Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/.github/workflows/ci.yml","dependencies":[{"id":7628883961,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7628883964,"package_name":"technote-space/get-diff-action","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":7628883966,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting.yml","sha":null,"kind":"manifest","created_at":"2023-02-13T19:31:50.449Z","updated_at":"2023-02-13T19:31:50.449Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/.github/workflows/linting.yml","dependencies":[{"id":7628886143,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7628886144,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7628886145,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7628886146,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7628886147,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":7628886148,"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":"2023-02-13T19:31:50.687Z","updated_at":"2023-02-13T19:31:50.687Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/.github/workflows/linting_comment.yml","dependencies":[{"id":7628889268,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7628889269,"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":"2023-09-23T11:14:08.485Z","updated_at":"2023-09-23T11:14:08.485Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/.github/workflows/clean-up.yml","dependencies":[{"id":13897779575,"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":"2023-09-23T11:14:09.073Z","updated_at":"2023-09-23T11:14:09.073Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/.github/workflows/fix-linting.yml","dependencies":[{"id":13897780559,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":13897780560,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/local/extract_communities/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:11.278Z","updated_at":"2023-09-23T11:14:11.278Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/local/extract_communities/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/local/multiqc_community/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:12.483Z","updated_at":"2023-09-23T11:14:12.483Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/local/multiqc_community/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/local/net2communities/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:13.699Z","updated_at":"2023-09-23T11:14:13.699Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/local/net2communities/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/local/paf2net/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:14.718Z","updated_at":"2023-09-23T11:14:14.718Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/local/paf2net/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/local/split_approx_mappings_in_chunks/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:15.719Z","updated_at":"2023-09-23T11:14:15.719Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/local/split_approx_mappings_in_chunks/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/local/vg_deconstruct/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:16.162Z","updated_at":"2023-09-23T11:14:16.162Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/local/vg_deconstruct/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/gfaffix/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:16.563Z","updated_at":"2023-09-23T11:14:16.563Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/gfaffix/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:16.966Z","updated_at":"2023-09-23T11:14:16.966Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/odgi/build/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:17.165Z","updated_at":"2023-09-23T11:14:17.165Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/build/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/odgi/draw/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:17.216Z","updated_at":"2023-09-23T11:14:17.216Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/draw/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/odgi/layout/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:17.485Z","updated_at":"2023-09-23T11:14:17.485Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/layout/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/odgi/sort/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:17.758Z","updated_at":"2023-09-23T11:14:17.758Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/sort/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/odgi/squeeze/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:18.053Z","updated_at":"2023-09-23T11:14:18.053Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/squeeze/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/odgi/stats/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-23T11:14:18.226Z","updated_at":"2023-09-23T11:14:18.226Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/stats/meta.yml","dependencies":[]},{"ecosystem":"conda","filepath":"modules/nf-core/gfaffix/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:28.415Z","updated_at":"2024-03-14T11:42:28.415Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/gfaffix/environment.yml","dependencies":[{"id":16812533332,"package_name":"gfaffix","ecosystem":"conda","requirements":"0.1.5.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/multiqc/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:28.678Z","updated_at":"2024-03-14T11:42:28.678Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/multiqc/environment.yml","dependencies":[{"id":16812533543,"package_name":"multiqc","ecosystem":"conda","requirements":"1.20.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/odgi/build/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:29.166Z","updated_at":"2024-03-14T11:42:29.166Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/build/environment.yml","dependencies":[{"id":16812534844,"package_name":"odgi","ecosystem":"conda","requirements":"0.8.4.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/odgi/draw/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:29.807Z","updated_at":"2024-03-14T11:42:29.807Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/draw/environment.yml","dependencies":[{"id":16812535275,"package_name":"odgi","ecosystem":"conda","requirements":"0.8.4.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/odgi/layout/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:30.253Z","updated_at":"2024-03-14T11:42:30.253Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/layout/environment.yml","dependencies":[{"id":16812535285,"package_name":"odgi","ecosystem":"conda","requirements":"0.8.4.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/odgi/sort/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:30.295Z","updated_at":"2024-03-14T11:42:30.295Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/sort/environment.yml","dependencies":[{"id":16812535609,"package_name":"odgi","ecosystem":"conda","requirements":"0.8.4.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/odgi/squeeze/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:30.554Z","updated_at":"2024-03-14T11:42:30.554Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/squeeze/environment.yml","dependencies":[{"id":16812535849,"package_name":"odgi","ecosystem":"conda","requirements":"0.8.4.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/odgi/stats/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:30.613Z","updated_at":"2024-03-14T11:42:30.613Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/stats/environment.yml","dependencies":[{"id":16812535860,"package_name":"odgi","ecosystem":"conda","requirements":"0.8.4.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/odgi/unchop/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:30.656Z","updated_at":"2024-03-14T11:42:30.656Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/unchop/environment.yml","dependencies":[{"id":16812535863,"package_name":"odgi","ecosystem":"conda","requirements":"0.8.4.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/odgi/view/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:30.713Z","updated_at":"2024-03-14T11:42:30.713Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/view/environment.yml","dependencies":[{"id":16812536550,"package_name":"odgi","ecosystem":"conda","requirements":"0.8.4.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/odgi/viz/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:30.864Z","updated_at":"2024-03-14T11:42:30.864Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/viz/environment.yml","dependencies":[{"id":16812537228,"package_name":"odgi","ecosystem":"conda","requirements":"0.8.4.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/odgi/unchop/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T17:23:36.694Z","updated_at":"2024-01-29T17:23:36.694Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/unchop/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/odgi/view/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T17:23:36.698Z","updated_at":"2024-01-29T17:23:36.698Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/view/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/odgi/viz/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T17:23:36.702Z","updated_at":"2024-01-29T17:23:36.702Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/odgi/viz/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/faidx/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T17:23:36.705Z","updated_at":"2024-01-29T17:23:36.705Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/samtools/faidx/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/seqwish/induce/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T17:23:36.709Z","updated_at":"2024-01-29T17:23:36.709Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/seqwish/induce/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/smoothxg/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T17:23:36.713Z","updated_at":"2024-01-29T17:23:36.713Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/smoothxg/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tabix/bgzip/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T17:23:36.717Z","updated_at":"2024-01-29T17:23:36.717Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/tabix/bgzip/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/wfmash/meta.yml","sha":null,"kind":"manifest","created_at":"2024-01-29T17:23:36.721Z","updated_at":"2024-01-29T17:23:36.721Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/wfmash/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2024-01-29T17:23:36.725Z","updated_at":"2024-01-29T17:23:36.725Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/pyproject.toml","dependencies":[]},{"ecosystem":"conda","filepath":"modules/nf-core/samtools/faidx/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:30.939Z","updated_at":"2024-03-14T11:42:30.939Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/samtools/faidx/environment.yml","dependencies":[{"id":16812537597,"package_name":"htslib","ecosystem":"conda","requirements":"1.19.1.*","direct":true,"kind":"runtime","optional":false},{"id":16812537599,"package_name":"samtools","ecosystem":"conda","requirements":"1.19.2.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/seqwish/induce/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:31.372Z","updated_at":"2024-03-14T11:42:31.372Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/seqwish/induce/environment.yml","dependencies":[{"id":16812537792,"package_name":"seqwish","ecosystem":"conda","requirements":"0.7.9.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/smoothxg/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:32.431Z","updated_at":"2024-03-14T11:42:32.431Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/smoothxg/environment.yml","dependencies":[{"id":16812538270,"package_name":"smoothxg","ecosystem":"conda","requirements":"0.7.2.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/tabix/bgzip/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:32.702Z","updated_at":"2024-03-14T11:42:32.702Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/tabix/bgzip/environment.yml","dependencies":[{"id":16812539284,"package_name":"tabix","ecosystem":"conda","requirements":"1.11.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/wfmash/environment.yml","sha":null,"kind":"manifest","created_at":"2024-03-14T11:42:33.563Z","updated_at":"2024-03-14T11:42:33.563Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/modules/nf-core/wfmash/environment.yml","dependencies":[{"id":16812539704,"package_name":"wfmash","ecosystem":"conda","requirements":"0.12.6.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/download_pipeline.yml","sha":null,"kind":"manifest","created_at":"2024-02-29T17:40:47.457Z","updated_at":"2024-02-29T17:40:47.457Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/.github/workflows/download_pipeline.yml","dependencies":[{"id":16523589360,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8","direct":true,"kind":"composite","optional":false},{"id":16523589361,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"0a5c61591373683505ea898e09a3ea4f39ef2b9c","direct":true,"kind":"composite","optional":false},{"id":16523589362,"package_name":"eWaterCycle/setup-singularity","ecosystem":"actions","requirements":"931d4e31109e875b13309ae1d07c70ca8fbc8537","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/release-announcements.yml","sha":null,"kind":"manifest","created_at":"2024-02-29T17:40:47.475Z","updated_at":"2024-02-29T17:40:47.475Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/.github/workflows/release-announcements.yml","dependencies":[{"id":16523589365,"package_name":"rzr/fediverse-action","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false},{"id":16523589366,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"0a5c61591373683505ea898e09a3ea4f39ef2b9c","direct":true,"kind":"composite","optional":false},{"id":16523589367,"package_name":"zentered/bluesky-post-action","ecosystem":"actions","requirements":"80dbe0a7697de18c15ad22f4619919ceb5ccf597","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2024-02-29T17:40:57.782Z","updated_at":"2024-02-29T17:40:57.782Z","repository_link":"https://github.com/nf-core/pangenome/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":"2024-02-29T17:40:57.786Z","updated_at":"2024-02-29T17:40:57.786Z","repository_link":"https://github.com/nf-core/pangenome/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":"2024-02-29T17:40:57.792Z","updated_at":"2024-02-29T17:40:57.792Z","repository_link":"https://github.com/nf-core/pangenome/blob/master/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml","dependencies":[]}],"score":6.742880635791902,"created_at":"2025-09-04T15:51:18.687Z","updated_at":"2025-10-07T08:17:38.744Z","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.8202636","https://doi.org/10.1093/bioinformatics/btae609","https://dx.doi.org/10.1038/s41587-020-0439-x"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["metagenomics","pipelines","workflows","bioinformatics","assembly","nanopore","dsl2","nf-test","annotation","long-read-sequencing"],"project_url":"https://science.ecosyste.ms/api/v1/projects/43575","html_url":"https://science.ecosyste.ms/projects/43575","bibtex_url":"https://science.ecosyste.ms/projects/43575/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/43575/export.apalike"}