{"id":36332,"name":"ampliseq","description":"Amplicon sequencing analysis workflow using DADA2 and QIIME2","url":"https://github.com/nf-core/ampliseq","last_synced_at":"2025-09-05T07:05:19.493Z","repository":{"id":33261773,"uuid":"150448201","full_name":"nf-core/ampliseq","owner":"nf-core","description":"Amplicon sequencing analysis workflow using DADA2 and QIIME2","archived":false,"fork":false,"pushed_at":"2025-08-21T06:47:26.000Z","size":18347,"stargazers_count":213,"open_issues_count":21,"forks_count":141,"subscribers_count":165,"default_branch":"master","last_synced_at":"2025-08-21T08:45:54.718Z","etag":null,"topics":["16s","18s","amplicon-sequencing","edna","illumina","iontorrent","its","metabarcoding","metagenomics","microbiome","nextflow","nf-core","pacbio","pipeline","qiime2","rrna","taxonomic-classification","taxonomic-profiling","workflow"],"latest_commit_sha":null,"homepage":"https://nf-co.re/ampliseq","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":"2018-09-26T15:24:54.000Z","updated_at":"2025-08-17T20:53:36.000Z","dependencies_parsed_at":"2023-10-19T08:24:25.928Z","dependency_job_id":"2064363e-2575-4339-97ac-3ef94732d1dd","html_url":"https://github.com/nf-core/ampliseq","commit_stats":{"total_commits":1634,"total_committers":39,"mean_commits":41.8974358974359,"dds":0.6181150550795593,"last_synced_commit":"4e48b7100302e2576ac1be2ccc7d464253e9d20e"},"previous_names":[],"tags_count":27,"template":false,"template_full_name":null,"purl":"pkg:github/nf-core/ampliseq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fampliseq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fampliseq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fampliseq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fampliseq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core","download_url":"https://codeload.github.com/nf-core/ampliseq/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fampliseq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273723195,"owners_count":25156304,"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":1317654,"full_name":"nf-core/ampliseq","default_branch":"master","committers":[{"name":"d4straub","email":"daniel.straub@uni-tuebingen.de","login":null,"count":624},{"name":"daniel","email":"d4straub@gmail.com","login":null,"count":237},{"name":"jtangrot","email":"jeanette.tangrot@umu.se","login":null,"count":223},{"name":"Alexander Peltzer","email":"alex.peltzer@gmail.com","login":null,"count":110},{"name":"Daniel Straub","email":"42973691+d4straub","login":"d4straub","count":83},{"name":"Daniel Lundin","email":"matricaria.suaveolens@gmail.com","login":null,"count":57},{"name":"Alexander Peltzer","email":"alexander.peltzer@uni-tuebingen.de","login":null,"count":36},{"name":"DiegoBrambilla","email":"diego.brambilla@lnu.se","login":null,"count":32},{"name":"Emelie Nilsso","email":"emelie.nilsson@lnu.se","login":null,"count":26},{"name":"Daniel Lundin","email":"erik.rikard.daniel@gmail.com","login":null,"count":24},{"name":"Sateesh Peri","email":"perisateesh@gmail.com","login":null,"count":24},{"name":"nf-core-bot","email":"core@nf-co.re","login":null,"count":24},{"name":"johnne","email":"john.sundh@scilifelab.se","login":null,"count":14},{"name":"DiegoBrambilla","email":"36502951+DiegoBrambilla","login":"DiegoBrambilla","count":13},{"name":"lokeshbio","email":"lokesh.cbt@gmail.com","login":null,"count":13},{"name":"Till Englert","email":"till.englert96@gmail.com","login":null,"count":13},{"name":"Adam Bennett","email":"adbennett@minderoo.org","login":null,"count":12},{"name":"maxulysse","email":"max.u.garcia@gmail.com","login":null,"count":12},{"name":"Asaf Peer","email":"asafpr@gmail.com","login":null,"count":10},{"name":"Alexander Peltzer","email":"apeltzer","login":"apeltzer","count":8},{"name":"Adam Bennett","email":"43841526+a4000","login":"a4000","count":7},{"name":"Sam Minot","email":"sminot@fredhutch.org","login":null,"count":5},{"name":"Daniel Lundin","email":"daniel.lundin@lnu.se","login":null,"count":4},{"name":"Venkat Malladi","email":"vmalladi@microsoft.com","login":null,"count":3},{"name":"PhilPalmer","email":"phil.palmer.email@gmail.com","login":null,"count":2},{"name":"drpatelh","email":"drhpatel@gmail.com","login":null,"count":2},{"name":"Colin Davenport","email":"colindaven@hotmail.com","login":null,"count":2},{"name":"Asaf Peer","email":"asafp@mybiotix.com","login":null,"count":2},{"name":"Phil Ewels","email":"phil.ewels@scilifelab.se","login":null,"count":2},{"name":"dariader","email":"dary.spb@gmail.com","login":null,"count":1},{"name":"runner","email":"runner@fv-az98","login":null,"count":1},{"name":"kevinmenden","email":"kevin.menden@t-online.de","login":null,"count":1},{"name":"Gisela Gabernet","email":"gisela.gabernet@gmail.com","login":null,"count":1},{"name":"Travis CI User","email":"travis@example.org","login":"invalid-email-address","count":1},{"name":"runner","email":"runner@fv-az60","login":null,"count":1},{"name":"Alexander Peltzer","email":"alexanderpeltzer@alexanders-mbp.am10.uni-tuebingen.de","login":null,"count":1},{"name":"Alexander Peltzer","email":"alexanderpeltzer@Alexanders-MBP.fritz.box","login":null,"count":1},{"name":"Harshil Patel","email":"drpatelh","login":"drpatelh","count":1},{"name":"Venkat Malladi","email":"vsmalladi@gmail.com","login":null,"count":1}],"total_commits":1634,"total_committers":39,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":41.8974358974359,"dds":0.6181150550795593,"past_year_committers":[{"name":"daniel","email":"d4straub@gmail.com","login":null,"count":237},{"name":"jtangrot","email":"jeanette.tangrot@umu.se","login":null,"count":115},{"name":"Daniel Straub","email":"42973691+d4straub","login":"d4straub","count":26},{"name":"d4straub","email":"daniel.straub@uni-tuebingen.de","login":null,"count":24},{"name":"Sateesh Peri","email":"perisateesh@gmail.com","login":null,"count":24},{"name":"johnne","email":"john.sundh@scilifelab.se","login":null,"count":14},{"name":"Till Englert","email":"till.englert96@gmail.com","login":null,"count":13},{"name":"lokeshbio","email":"lokesh.cbt@gmail.com","login":null,"count":13},{"name":"Adam Bennett","email":"adbennett@minderoo.org","login":null,"count":12},{"name":"maxulysse","email":"max.u.garcia@gmail.com","login":null,"count":9},{"name":"Adam Bennett","email":"43841526+a4000","login":"a4000","count":7},{"name":"Sam Minot","email":"sminot@fredhutch.org","login":null,"count":5},{"name":"nf-core-bot","email":"core@nf-co.re","login":null,"count":5},{"name":"Daniel Lundin","email":"erik.rikard.daniel@gmail.com","login":null,"count":4},{"name":"dariader","email":"dary.spb@gmail.com","login":null,"count":1}],"past_year_total_commits":509,"past_year_total_committers":15,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":33.93333333333333,"past_year_dds":0.5343811394891945,"last_synced_at":"2023-11-04T18:32:39.445Z","last_synced_commit":"4e48b7100302e2576ac1be2ccc7d464253e9d20e","created_at":"2023-06-15T18:09:19.551Z","updated_at":"2023-11-04T18:32:39.446Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fampliseq/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/ampliseq","html_url":"https://github.com/nf-core/ampliseq","last_synced_at":"2025-08-31T09:10:02.764Z","status":null,"issues_count":101,"pull_requests_count":146,"avg_time_to_close_issue":11902763.814814815,"avg_time_to_close_pull_request":664927.3464566929,"issues_closed_count":81,"pull_requests_closed_count":127,"pull_request_authors_count":25,"issue_authors_count":55,"avg_comments_per_issue":4.1683168316831685,"avg_comments_per_pull_request":2.116438356164384,"merged_pull_requests_count":118,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":30,"past_year_pull_requests_count":55,"past_year_avg_time_to_close_issue":2848277.6315789474,"past_year_avg_time_to_close_pull_request":939500.3513513514,"past_year_issues_closed_count":19,"past_year_pull_requests_closed_count":37,"past_year_pull_request_authors_count":18,"past_year_issue_authors_count":17,"past_year_avg_comments_per_issue":2.2666666666666666,"past_year_avg_comments_per_pull_request":1.4181818181818182,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":34,"created_at":"2023-06-15T18:11:07.704Z","updated_at":"2025-09-03T04:58:16.668Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fampliseq","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fampliseq/issues","issue_labels_count":{"bug":67,"enhancement":56,"documentation":2,"unconfirmed":1,"not urgent":1},"pull_request_labels_count":{"WIP":1,"enhancement":1,"bug":1,"documentation":1},"issue_author_associations_count":{"NONE":99,"COLLABORATOR":24,"MEMBER":16,"CONTRIBUTOR":8},"pull_request_author_associations_count":{"COLLABORATOR":132,"NONE":29,"MEMBER":27,"CONTRIBUTOR":22},"issue_authors":{"d4straub":24,"erikrikarddaniel":15,"a4000":5,"marwa38":4,"andand":3,"jtangrot":3,"agrier-wcm":3,"Sofokli5":3,"skose82":3,"ulrichmarkus":2,"Dedaniya08":2,"pragermh":2,"sgaleraalq":2,"lch14forever":2,"enriiquee":2,"pehenrique":2,"eperezv":2,"nagendraKU":2,"tom-brekke":2,"SergeWielhouwer":2,"lbiernot":1,"prototaxites":1,"bioinfogaby":1,"VeronicRojo":1,"aimirza":1,"ohan-Bioinfo":1,"tjcreedy":1,"kesava31":1,"weber8thomas":1,"aqsakhalid03":1,"amalacrino":1,"CristianNa":1,"sajjadasaf":1,"hkaspersen":1,"scheckley":1,"ShareiFae":1,"linshizuowei":1,"tremblayemilie":1,"ebete":1,"dbu008":1,"luozhy88":1,"himamura2":1,"kjurdzinski":1,"brovolia":1,"x-rv":1,"srikanthkris":1,"ilwookkim":1,"susheelbhanu":1,"nf-core-bot":1,"micrrwd":1,"emmastrand":1,"lam-c":1,"vaulot":1,"bark9299":1,"Lumimar":1,"PedroDaPos":1,"danilodileo":1,"dixi06":1,"Juke34":1,"kdivilov":1,"chuan-wang":1,"hjarnek":1,"annotatebio":1,"davised":1,"johnne":1,"jambler24":1,"freemutation":1,"amakunin":1,"WangLab-SCSIO":1,"gbaiao":1,"sonalhenson":1,"Ste40":1,"TuomasBorman":1,"asgarhussain":1,"BCArg":1,"DiegoBrambilla":1,"AnotherSimon":1,"petemeng":1,"Truongphi20":1,"Luke-ebbis":1,"ysayyed11":1,"JayalalKJ":1},"pull_request_authors":{"d4straub":132,"nf-core-bot":17,"jtangrot":14,"erikrikarddaniel":7,"lokeshbio":3,"danilodileo":3,"dariader":2,"weber8thomas":2,"nhenry50":2,"Sofokli5":2,"vaulot":2,"sateeshperi":2,"a4000":2,"sminot":2,"tillenglert":2,"chan-98":2,"ilwookkim":1,"aslangabriel99":1,"robsyme":1,"maxulysse":1,"StuntsPT":1,"tom-brekke":1,"samuell":1,"georgiakes":1,"TuomasBorman":1,"Dedaniya08":1,"mashehu":1,"4less":1,"pinin4fjords":1,"johnne":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10087320,"issues_count":31306968,"pull_requests_count":96469683,"authors_count":10696025,"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":19,"enhancement":15,"unconfirmed":1},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"NONE":31,"COLLABORATOR":11,"MEMBER":3,"CONTRIBUTOR":2},"past_year_pull_request_author_associations_count":{"COLLABORATOR":38,"MEMBER":14,"NONE":13,"CONTRIBUTOR":8},"past_year_issue_authors":{"d4straub":11,"marwa38":4,"Sofokli5":3,"tom-brekke":2,"Dedaniya08":2,"erikrikarddaniel":2,"nagendraKU":2,"ysayyed11":1,"VeronicRojo":1,"TuomasBorman":1,"tremblayemilie":1,"sonalhenson":1,"sajjadasaf":1,"PedroDaPos":1,"ohan-Bioinfo":1,"nf-core-bot":1,"micrrwd":1,"Lumimar":1,"Luke-ebbis":1,"kesava31":1,"Juke34":1,"jtangrot":1,"ebete":1,"dbu008":1,"danilodileo":1,"CristianNa":1,"brovolia":1,"agrier-wcm":1},"past_year_pull_request_authors":{"d4straub":38,"nf-core-bot":9,"jtangrot":3,"erikrikarddaniel":3,"chan-98":2,"Sofokli5":2,"nhenry50":2,"weber8thomas":2,"tom-brekke":1,"StuntsPT":1,"samuell":1,"georgiakes":1,"Dedaniya08":1,"TuomasBorman":1,"mashehu":1,"4less":1,"robsyme":1,"danilodileo":1,"pinin4fjords":1,"lokeshbio":1},"maintainers":[{"login":"d4straub","count":156,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/d4straub"},{"login":"erikrikarddaniel","count":22,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/erikrikarddaniel"},{"login":"nf-core-bot","count":18,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"pinin4fjords","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/pinin4fjords"},{"login":"georgiakes","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/georgiakes"},{"login":"maxulysse","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/maxulysse"}],"active_maintainers":[{"login":"d4straub","count":49,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/d4straub"},{"login":"nf-core-bot","count":10,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"erikrikarddaniel","count":5,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/erikrikarddaniel"},{"login":"pinin4fjords","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/pinin4fjords"},{"login":"georgiakes","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/georgiakes"}]},"events":{"total":{"CreateEvent":14,"ReleaseEvent":3,"IssuesEvent":86,"WatchEvent":26,"DeleteEvent":16,"IssueCommentEvent":286,"PushEvent":64,"PullRequestReviewEvent":139,"PullRequestReviewCommentEvent":86,"PullRequestEvent":124,"ForkEvent":28},"last_year":{"CreateEvent":14,"ReleaseEvent":3,"IssuesEvent":86,"WatchEvent":26,"DeleteEvent":16,"IssueCommentEvent":286,"PushEvent":64,"PullRequestReviewEvent":139,"PullRequestReviewCommentEvent":86,"PullRequestEvent":124,"ForkEvent":28}},"keywords":["16s","18s","amplicon-sequencing","edna","illumina","iontorrent","its","metabarcoding","metagenomics","microbiome","nextflow","nf-core","pacbio","pipeline","qiime2","rrna","taxonomic-classification","taxonomic-profiling","workflow"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/awsfulltest.yml","sha":null,"kind":"manifest","created_at":"2023-01-15T00:15:22.856Z","updated_at":"2023-01-15T00:15:22.856Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/.github/workflows/awsfulltest.yml","dependencies":[{"id":6909569614,"package_name":"nf-core/tower-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":6909569615,"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":"2023-01-15T00:15:23.606Z","updated_at":"2023-01-15T00:15:23.606Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/.github/workflows/awstest.yml","dependencies":[{"id":6909570949,"package_name":"nf-core/tower-action","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":6909570950,"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":"2023-01-15T00:15:24.027Z","updated_at":"2023-01-15T00:15:24.027Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/.github/workflows/branch.yml","dependencies":[{"id":6909572485,"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":"2023-10-19T08:24:20.709Z","updated_at":"2023-10-19T08:24:20.709Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/.github/workflows/ci.yml","dependencies":[{"id":14261376585,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":14261376586,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":14261376587,"package_name":"mikepenz/action-junit-report","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/clean-up.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:20.858Z","updated_at":"2023-10-19T08:24:20.858Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/.github/workflows/clean-up.yml","dependencies":[{"id":14261376588,"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":"2023-10-19T08:24:20.929Z","updated_at":"2023-10-19T08:24:20.929Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/.github/workflows/fix-linting.yml","dependencies":[{"id":14261376589,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":14261376590,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:21.004Z","updated_at":"2023-10-19T08:24:21.004Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/.github/workflows/linting.yml","dependencies":[{"id":14261376591,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":14261376592,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":14261376593,"package_name":"psf/black","ecosystem":"actions","requirements":"stable","direct":true,"kind":"composite","optional":false},{"id":14261376594,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":14261376595,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":14261376596,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":14261376597,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting_comment.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:21.136Z","updated_at":"2023-10-19T08:24:21.136Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/.github/workflows/linting_comment.yml","dependencies":[{"id":14261376598,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":14261376599,"package_name":"marocchino/sticky-pull-request-comment","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/custom/dumpsoftwareversions/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:21.244Z","updated_at":"2023-10-19T08:24:21.244Z","repository_link":"https://github.com/nf-core/ampliseq/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":"2023-10-19T08:24:21.288Z","updated_at":"2023-10-19T08:24:21.288Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/cutadapt/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/epang/place/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:21.349Z","updated_at":"2023-10-19T08:24:21.349Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/epang/place/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/epang/split/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:21.432Z","updated_at":"2023-10-19T08:24:21.432Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/epang/split/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastqc/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:21.511Z","updated_at":"2023-10-19T08:24:21.511Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/gappa/examineassign/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:21.564Z","updated_at":"2023-10-19T08:24:21.564Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/gappa/examineassign/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/gappa/examinegraft/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:22.046Z","updated_at":"2023-10-19T08:24:22.046Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/gappa/examinegraft/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/gappa/examineheattree/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:22.951Z","updated_at":"2023-10-19T08:24:22.951Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/gappa/examineheattree/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/hmmer/eslalimask/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:23.957Z","updated_at":"2023-10-19T08:24:23.957Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/hmmer/eslalimask/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/hmmer/eslreformat/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:24.955Z","updated_at":"2023-10-19T08:24:24.955Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/hmmer/eslreformat/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/hmmer/hmmalign/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:25.313Z","updated_at":"2023-10-19T08:24:25.313Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/hmmer/hmmalign/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/hmmer/hmmbuild/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:25.367Z","updated_at":"2023-10-19T08:24:25.367Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/hmmer/hmmbuild/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/mafft/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:25.424Z","updated_at":"2023-10-19T08:24:25.424Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/mafft/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:25.460Z","updated_at":"2023-10-19T08:24:25.460Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/vsearch/sintax/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:25.535Z","updated_at":"2023-10-19T08:24:25.535Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/vsearch/sintax/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/vsearch/usearchglobal/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:25.625Z","updated_at":"2023-10-19T08:24:25.625Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/modules/nf-core/vsearch/usearchglobal/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:25.704Z","updated_at":"2023-10-19T08:24:25.704Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2023-10-19T08:24:25.773Z","updated_at":"2023-10-19T08:24:25.773Z","repository_link":"https://github.com/nf-core/ampliseq/blob/master/pyproject.toml","dependencies":[]}],"score":9.118882761487349,"created_at":"2025-09-04T15:51:09.932Z","updated_at":"2025-10-07T08:15:01.637Z","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.1493841","https://doi.org/10.3389/fmicb.2020.550420","https://doi.org/10.6084/m9.figshare.16871008.v1","https://doi.org/10.1038/nmeth.3869","https://doi.org/10.1101/074161","https://doi.org/10.1186/s13059-019-1891-0","https://doi.org/10.12688/f1000research.26669.2","https://dx.doi.org/10.1038/s41587-020-0439-x"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["workflows","nf-test","dsl2","pipelines","atac-seq","chromatin-accessibiity","qc","nanopore","demultiplexing","alignment"],"project_url":"https://science.ecosyste.ms/api/v1/projects/36332","html_url":"https://science.ecosyste.ms/projects/36332","bibtex_url":"https://science.ecosyste.ms/projects/36332/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/36332/export.apalike"}