{"id":3491,"name":"bpertussis-ciwgs","description":"Culture-Independent Whole Genome Sequencing (CIWGS) Read Filter Pipeline 🧪🧬🖥️","url":"https://github.com/cdcgov/bpertussis-ciwgs","last_synced_at":"2025-09-04T17:03:40.506Z","repository":{"id":209700291,"uuid":"721302470","full_name":"CDCgov/bpertussis-ciwgs","owner":"CDCgov","description":"Culture-Independent Whole Genome Sequencing (CIWGS) Read Filter Pipeline 🧪🧬🖥️","archived":false,"fork":false,"pushed_at":"2024-12-10T14:57:39.000Z","size":57019,"stargazers_count":2,"open_issues_count":1,"forks_count":2,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-07-30T17:36:38.966Z","etag":null,"topics":["bioinformatics","genomic-surveillance","nextflow","pertussis","wgs"],"latest_commit_sha":null,"homepage":"","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/CDCgov.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":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-11-20T19:23:03.000Z","updated_at":"2025-01-11T10:40:51.000Z","dependencies_parsed_at":"2023-12-11T14:42:37.767Z","dependency_job_id":"e42c4b4d-9f78-4f61-8faf-a284a25f0fcf","html_url":"https://github.com/CDCgov/bpertussis-ciwgs","commit_stats":{"total_commits":15,"total_committers":2,"mean_commits":7.5,"dds":"0.19999999999999996","last_synced_commit":"0d967cc9f88b9e7d74769459b5ba8cc24389fe35"},"previous_names":["cdcgov/bpertussis-ciwgs"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/CDCgov/bpertussis-ciwgs","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fbpertussis-ciwgs","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fbpertussis-ciwgs/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fbpertussis-ciwgs/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fbpertussis-ciwgs/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CDCgov","download_url":"https://codeload.github.com/CDCgov/bpertussis-ciwgs/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2Fbpertussis-ciwgs/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273641906,"owners_count":25142248,"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":"2025-09-04T02:00:08.968Z","response_time":61,"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":"CDCgov","name":"Centers for Disease Control and Prevention","uuid":"12104975","kind":"organization","description":"CDC's collaborative software projects to protect America from health, safety, and security threats, both foreign and in the U.S.","email":"data@cdc.gov","website":"http://open.cdc.gov/","location":"Atlanta, GA","twitter":"CDCgov","company":null,"icon_url":"https://avatars.githubusercontent.com/u/12104975?v=4","repositories_count":114,"last_synced_at":"2023-03-01T17:45:31.221Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/CDCgov","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-12T14:08:08.128Z","updated_at":"2023-03-01T17:45:31.316Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CDCgov","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CDCgov/repositories"},"packages":null,"commits":{"id":1453876,"full_name":"cdcgov/bpertussis-ciwgs","default_branch":"master","committers":[{"name":"Mike Weigand","email":"yrh8@cdc.gov","login":"mikeyweigand","count":15}],"total_commits":15,"total_committers":1,"total_bot_commits":0,"total_bot_committers":0,"mean_commits":15.0,"dds":0.0,"past_year_committers":[],"past_year_total_commits":0,"past_year_total_committers":0,"past_year_total_bot_commits":0,"past_year_total_bot_committers":0,"past_year_mean_commits":0.0,"past_year_dds":0.0,"last_synced_at":"2025-07-30T16:38:13.487Z","last_synced_commit":"0d967cc9f88b9e7d74769459b5ba8cc24389fe35","created_at":"2023-12-08T00:09:23.715Z","updated_at":"2025-07-30T16:38:13.487Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/cdcgov%2Fbpertussis-ciwgs/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-04T00:00:25.936Z","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":"cdcgov/bpertussis-ciwgs","html_url":"https://github.com/cdcgov/bpertussis-ciwgs","last_synced_at":"2025-07-30T16:40:13.203Z","status":"error","issues_count":1,"pull_requests_count":2,"avg_time_to_close_issue":17595659.0,"avg_time_to_close_pull_request":21.0,"issues_closed_count":1,"pull_requests_closed_count":1,"pull_request_authors_count":1,"issue_authors_count":1,"avg_comments_per_issue":1.0,"avg_comments_per_pull_request":0.0,"merged_pull_requests_count":1,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":1,"past_year_pull_requests_count":1,"past_year_avg_time_to_close_issue":17595659.0,"past_year_avg_time_to_close_pull_request":null,"past_year_issues_closed_count":1,"past_year_pull_requests_closed_count":0,"past_year_pull_request_authors_count":1,"past_year_issue_authors_count":1,"past_year_avg_comments_per_issue":1.0,"past_year_avg_comments_per_pull_request":0.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":0,"created_at":"2023-12-08T00:09:24.372Z","updated_at":"2025-09-01T15:28:35.873Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/cdcgov%2Fbpertussis-ciwgs","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/cdcgov%2Fbpertussis-ciwgs/issues","issue_labels_count":{"bug":1},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":1},"pull_request_author_associations_count":{"COLLABORATOR":2},"issue_authors":{"wchen190":1},"pull_request_authors":{"mikeyweigand":2},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-04T00:00:25.939Z","repositories_count":10079947,"issues_count":31294689,"pull_requests_count":96077738,"authors_count":10693120,"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":{},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{},"past_year_pull_request_author_associations_count":{"COLLABORATOR":1},"past_year_issue_authors":{},"past_year_pull_request_authors":{"mikeyweigand":1},"maintainers":[{"login":"mikeyweigand","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mikeyweigand"}],"active_maintainers":[{"login":"mikeyweigand","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mikeyweigand"}]},"events":{"total":{"IssuesEvent":1,"WatchEvent":1,"PushEvent":1,"PullRequestEvent":1,"ForkEvent":3,"CreateEvent":1},"last_year":{"IssuesEvent":1,"WatchEvent":1,"PushEvent":1,"PullRequestEvent":1,"ForkEvent":3,"CreateEvent":1}},"keywords":["bioinformatics","genomic-surveillance","nextflow","pertussis","wgs"],"dependencies":[{"ecosystem":"cpan","filepath":"modules/local/dumpsoftwareversions/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:35.187Z","updated_at":"2023-12-11T14:42:35.187Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/local/dumpsoftwareversions/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/fastqc/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:35.299Z","updated_at":"2023-12-11T14:42:35.299Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:35.379Z","updated_at":"2023-12-11T14:42:35.379Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/nf-core/blast/blastn/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:35.435Z","updated_at":"2023-12-11T14:42:35.435Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/nf-core/blast/blastn/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/nf-core/bowtie2/align/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:35.549Z","updated_at":"2023-12-11T14:42:35.549Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/nf-core/bowtie2/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/nf-core/bowtie2/build/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:35.694Z","updated_at":"2023-12-11T14:42:35.694Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/nf-core/bowtie2/build/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/nf-core/quast/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:36.185Z","updated_at":"2023-12-11T14:42:36.185Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/nf-core/quast/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/nf-core/samtools/depth/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:36.784Z","updated_at":"2023-12-11T14:42:36.784Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/nf-core/samtools/depth/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/nf-core/samtools/fastq/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:36.866Z","updated_at":"2023-12-11T14:42:36.866Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/nf-core/samtools/fastq/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/nf-core/samtools/fixmate/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:36.904Z","updated_at":"2023-12-11T14:42:36.904Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/nf-core/samtools/fixmate/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/nf-core/samtools/flagstat/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:37.090Z","updated_at":"2023-12-11T14:42:37.090Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/nf-core/samtools/flagstat/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/nf-core/samtools/index/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:37.318Z","updated_at":"2023-12-11T14:42:37.318Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/nf-core/samtools/index/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/nf-core/samtools/markdup/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:37.403Z","updated_at":"2023-12-11T14:42:37.403Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/nf-core/samtools/markdup/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/nf-core/samtools/sort/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:37.465Z","updated_at":"2023-12-11T14:42:37.465Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/nf-core/samtools/sort/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/modules/nf-core/samtools/view/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-11T14:42:37.627Z","updated_at":"2023-12-11T14:42:37.627Z","repository_link":"https://github.com/CDCgov/bpertussis-ciwgs/blob/master/modules/nf-core/modules/nf-core/samtools/view/meta.yml","dependencies":[]}],"score":1.0986122886681098,"created_at":"2025-09-04T15:50:08.077Z","updated_at":"2025-10-07T08:04:46.315Z","avatar_url":"https://github.com/CDCgov.png","language":"Nextflow","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1101/2023.12.08.570824","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/3491","html_url":"https://science.ecosyste.ms/projects/3491","bibtex_url":"https://science.ecosyste.ms/projects/3491/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/3491/export.apalike"}