{"id":35373,"name":"genomeqc","description":"Compare the quality of multiple genomes, along with their annotations.","url":"https://github.com/nf-core/genomeqc","last_synced_at":"2025-09-05T06:42:08.752Z","repository":{"id":258282599,"uuid":"862954512","full_name":"nf-core/genomeqc","owner":"nf-core","description":"Compare the quality of multiple genomes, along with their annotations.","archived":false,"fork":false,"pushed_at":"2025-08-28T10:11:42.000Z","size":2877,"stargazers_count":15,"open_issues_count":58,"forks_count":16,"subscribers_count":35,"default_branch":"dev","last_synced_at":"2025-08-28T17:28:43.257Z","etag":null,"topics":["bioinformatics","genome-assembly-evaluation","genomics","nextflow","nf-core","phylogenetic-trees","pipeline","quality-control"],"latest_commit_sha":null,"homepage":"https://nf-co.re/genomeqc","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":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATIONS.md","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2024-09-25T13:21:38.000Z","updated_at":"2025-08-07T13:54:08.000Z","dependencies_parsed_at":"2024-10-28T12:01:30.514Z","dependency_job_id":"6c50e519-55dd-40ed-85d8-e3c5d1060dfe","html_url":"https://github.com/nf-core/genomeqc","commit_stats":null,"previous_names":["eco-flow/genomeqc"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/nf-core/genomeqc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fgenomeqc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fgenomeqc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fgenomeqc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fgenomeqc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core","download_url":"https://codeload.github.com/nf-core/genomeqc/tar.gz/refs/heads/dev","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fgenomeqc/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273723207,"owners_count":25156303,"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":{"message":"Repository syncing started."},"issues_stats":{"full_name":"nf-core/genomeqc","html_url":"https://github.com/nf-core/genomeqc","last_synced_at":"2025-09-04T17:45:23.865Z","status":null,"issues_count":47,"pull_requests_count":39,"avg_time_to_close_issue":1080193.6,"avg_time_to_close_pull_request":854668.0434782609,"issues_closed_count":20,"pull_requests_closed_count":23,"pull_request_authors_count":11,"issue_authors_count":6,"avg_comments_per_issue":0.2765957446808511,"avg_comments_per_pull_request":1.0,"merged_pull_requests_count":18,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":47,"past_year_pull_requests_count":39,"past_year_avg_time_to_close_issue":1080193.6,"past_year_avg_time_to_close_pull_request":854668.0434782609,"past_year_issues_closed_count":20,"past_year_pull_requests_closed_count":23,"past_year_pull_request_authors_count":11,"past_year_issue_authors_count":6,"past_year_avg_comments_per_issue":0.2765957446808511,"past_year_avg_comments_per_pull_request":1.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":18,"created_at":"2025-08-29T14:24:43.481Z","updated_at":"2025-09-04T17:45:23.867Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fgenomeqc","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fgenomeqc/issues","issue_labels_count":{"enhancement":7,"bug":5},"pull_request_labels_count":{"enhancement":1},"issue_author_associations_count":{"CONTRIBUTOR":25,"COLLABORATOR":20,"NONE":2},"pull_request_author_associations_count":{"COLLABORATOR":14,"CONTRIBUTOR":12,"MEMBER":7,"NONE":6},"issue_authors":{"FernandoDuarteF":20,"chriswyatt1":17,"stephenturner":7,"hbadrane":1,"tanashreebioinfo":1,"Juke34":1},"pull_request_authors":{"FernandoDuarteF":14,"chriswyatt1":11,"nf-core-bot":6,"Juke34":1,"BenjaminATaylor":1,"SimonDMurray":1,"fperezcobos":1,"GallVp":1,"awanalkoerdi289":1,"LaurenHuet":1,"stephenturner":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":{"enhancement":7,"bug":5},"past_year_pull_request_labels_count":{"enhancement":1},"past_year_issue_author_associations_count":{"CONTRIBUTOR":25,"COLLABORATOR":20,"NONE":2},"past_year_pull_request_author_associations_count":{"COLLABORATOR":14,"CONTRIBUTOR":12,"MEMBER":7,"NONE":6},"past_year_issue_authors":{"FernandoDuarteF":20,"chriswyatt1":17,"stephenturner":7,"hbadrane":1,"Juke34":1,"tanashreebioinfo":1},"past_year_pull_request_authors":{"FernandoDuarteF":14,"chriswyatt1":11,"nf-core-bot":6,"Juke34":1,"SimonDMurray":1,"GallVp":1,"fperezcobos":1,"awanalkoerdi289":1,"BenjaminATaylor":1,"LaurenHuet":1,"stephenturner":1},"maintainers":[{"login":"FernandoDuarteF","count":34,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/FernandoDuarteF"},{"login":"nf-core-bot","count":6,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"GallVp","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/GallVp"}],"active_maintainers":[{"login":"FernandoDuarteF","count":34,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/FernandoDuarteF"},{"login":"nf-core-bot","count":6,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"GallVp","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/GallVp"}]},"events":{"total":{"IssuesEvent":85,"WatchEvent":15,"DeleteEvent":10,"IssueCommentEvent":131,"PushEvent":83,"PullRequestReviewEvent":49,"PullRequestReviewCommentEvent":82,"PullRequestEvent":67,"ForkEvent":11,"CreateEvent":19},"last_year":{"IssuesEvent":85,"WatchEvent":15,"DeleteEvent":10,"IssueCommentEvent":131,"PushEvent":83,"PullRequestReviewEvent":49,"PullRequestReviewCommentEvent":82,"PullRequestEvent":67,"ForkEvent":11,"CreateEvent":19}},"keywords":["bioinformatics","genome-assembly-evaluation","genomics","nextflow","nf-core","phylogenetic-trees","pipeline","quality-control"],"dependencies":[{"ecosystem":"cpan","filepath":"modules/nf-core/busco/busco/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-18T09:24:03.244Z","updated_at":"2024-10-18T09:24:03.244Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/busco/busco/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastqc/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-18T09:24:03.450Z","updated_at":"2024-10-18T09:24:03.450Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/gffread/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-18T09:24:03.782Z","updated_at":"2024-10-18T09:24:03.782Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/gffread/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-18T09:24:04.180Z","updated_at":"2024-10-18T09:24:04.180Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/ncbigenomedownload/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-18T09:24:04.440Z","updated_at":"2024-10-18T09:24:04.440Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/ncbigenomedownload/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/orthofinder/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-18T09:24:04.893Z","updated_at":"2024-10-18T09:24:04.893Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/orthofinder/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/pigz/uncompress/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-18T09:24:05.120Z","updated_at":"2024-10-18T09:24:05.120Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/pigz/uncompress/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-18T09:24:05.474Z","updated_at":"2024-10-18T09:24:05.474Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/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":"2024-10-18T09:24:05.892Z","updated_at":"2024-10-18T09:24:05.892Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/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":"2024-10-18T09:24:06.056Z","updated_at":"2024-10-18T09:24:06.056Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/seqkit/seq/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-19T00:57:35.975Z","updated_at":"2024-10-19T00:57:35.975Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/seqkit/seq/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/seqkit/sort/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-19T00:57:35.983Z","updated_at":"2024-10-19T00:57:35.983Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/seqkit/sort/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tidk/explore/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-19T00:57:35.988Z","updated_at":"2024-10-19T00:57:35.988Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/tidk/explore/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tidk/plot/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-19T00:57:35.993Z","updated_at":"2024-10-19T00:57:35.993Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/tidk/plot/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tidk/search/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-19T00:57:35.996Z","updated_at":"2024-10-19T00:57:35.996Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/tidk/search/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/fasta_explore_search_plot_tidk/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-19T00:57:36.000Z","updated_at":"2024-10-19T00:57:36.000Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/subworkflows/nf-core/fasta_explore_search_plot_tidk/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/agat/spstatistics/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-23T19:01:49.895Z","updated_at":"2024-10-23T19:01:49.895Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/agat/spstatistics/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/quast/meta.yml","sha":null,"kind":"manifest","created_at":"2024-10-23T19:01:50.075Z","updated_at":"2024-10-23T19:01:50.075Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/quast/meta.yml","dependencies":[]},{"ecosystem":"conda","filepath":"modules/nf-core/agat/spstatistics/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:21.032Z","updated_at":"2024-10-28T12:01:21.032Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/agat/spstatistics/environment.yml","dependencies":[{"id":20449358783,"package_name":"agat","ecosystem":"conda","requirements":"1.4.0.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/busco/busco/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:21.688Z","updated_at":"2024-10-28T12:01:21.688Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/busco/busco/environment.yml","dependencies":[{"id":20449358784,"package_name":"busco","ecosystem":"conda","requirements":"5.7.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/fastqc/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:23.039Z","updated_at":"2024-10-28T12:01:23.039Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/fastqc/environment.yml","dependencies":[{"id":20449358785,"package_name":"fastqc","ecosystem":"conda","requirements":"0.12.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/gffread/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:23.154Z","updated_at":"2024-10-28T12:01:23.154Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/gffread/environment.yml","dependencies":[{"id":20449358786,"package_name":"gffread","ecosystem":"conda","requirements":"0.12.7.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/multiqc/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:24.215Z","updated_at":"2024-10-28T12:01:24.215Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/multiqc/environment.yml","dependencies":[{"id":20449358787,"package_name":"multiqc","ecosystem":"conda","requirements":"1.21.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/ncbigenomedownload/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:24.440Z","updated_at":"2024-10-28T12:01:24.440Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/ncbigenomedownload/environment.yml","dependencies":[{"id":20449358788,"package_name":"ncbi-genome-download","ecosystem":"conda","requirements":"0.3.3.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/orthofinder/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:25.071Z","updated_at":"2024-10-28T12:01:25.071Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/orthofinder/environment.yml","dependencies":[{"id":20449358789,"package_name":"diamond","ecosystem":"conda","requirements":"2.1.9.*","direct":true,"kind":"runtime","optional":false},{"id":20449358790,"package_name":"orthofinder","ecosystem":"conda","requirements":"2.5.5.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/quast/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:26.937Z","updated_at":"2024-10-28T12:01:26.937Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/quast/environment.yml","dependencies":[{"id":20449358791,"package_name":"quast","ecosystem":"conda","requirements":"5.2.0.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"modules/nf-core/seqkit/seq/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:27.983Z","updated_at":"2024-10-28T12:01:27.983Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/seqkit/seq/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/seqkit/sort/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:28.036Z","updated_at":"2024-10-28T12:01:28.036Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/seqkit/sort/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/tidk/explore/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:28.086Z","updated_at":"2024-10-28T12:01:28.086Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/tidk/explore/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/tidk/plot/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:28.134Z","updated_at":"2024-10-28T12:01:28.134Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/tidk/plot/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/tidk/search/environment.yml","sha":null,"kind":"manifest","created_at":"2024-10-28T12:01:28.252Z","updated_at":"2024-10-28T12:01:28.252Z","repository_link":"https://github.com/nf-core/genomeqc/blob/dev/modules/nf-core/tidk/search/environment.yml","dependencies":[]}],"score":null,"created_at":"2025-09-04T15:51:08.844Z","updated_at":"2025-10-07T08:14:42.683Z","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.XXXXXXX","https://doi.org/10.5281/zenodo.XXXXXX","https://dx.doi.org/10.1038/s41587-020-0439-x"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/35373","html_url":"https://science.ecosyste.ms/projects/35373","bibtex_url":"https://science.ecosyste.ms/projects/35373/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/35373/export.apalike"}