{"id":36695,"name":"ascc","description":"A Nextflow DSL2 pipeline for the identification of cobiont and contaminating sequences using fasta and pacbio data.","url":"https://github.com/sanger-tol/ascc","last_synced_at":"2025-09-05T07:11:59.537Z","repository":{"id":180677515,"uuid":"663107966","full_name":"sanger-tol/ascc","owner":"sanger-tol","description":"A Nextflow DSL2 pipeline for the identification of cobiont and contaminating sequences using fasta and pacbio data.","archived":false,"fork":false,"pushed_at":"2025-08-28T08:46:48.000Z","size":16265,"stargazers_count":5,"open_issues_count":24,"forks_count":0,"subscribers_count":7,"default_branch":"main","last_synced_at":"2025-08-28T15:31:52.421Z","etag":null,"topics":["genomics","nextflow","pipeline"],"latest_commit_sha":null,"homepage":"https://pipelines.tol.sanger.ac.uk/ascc","language":"Python","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/sanger-tol.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","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":"2023-07-06T15:09:02.000Z","updated_at":"2025-08-06T15:11:56.000Z","dependencies_parsed_at":"2023-10-11T12:10:27.741Z","dependency_job_id":"ed883566-1b54-4ee9-b62d-697ba8633d7d","html_url":"https://github.com/sanger-tol/ascc","commit_stats":null,"previous_names":["sanger-tol/ascc"],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/sanger-tol/ascc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fascc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fascc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fascc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fascc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sanger-tol","download_url":"https://codeload.github.com/sanger-tol/ascc/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fascc/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273723736,"owners_count":25156402,"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":"sanger-tol","name":"Tree of Life programme","uuid":"70318076","kind":"organization","description":"The Tree of Life Programme investigates the diversity of complex organisms (eukaryotes) through sequencing and cellular technology","email":null,"website":"https://www.sanger.ac.uk/programme/tree-of-life/","location":"United Kingdom","twitter":"sangertol","company":null,"icon_url":"https://avatars.githubusercontent.com/u/70318076?v=4","repositories_count":15,"last_synced_at":"2023-03-04T17:33:58.308Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/sanger-tol","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-14T21:51:33.911Z","updated_at":"2023-03-04T17:33:58.332Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sanger-tol","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sanger-tol/repositories"},"packages":null,"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"sanger-tol/ascc","html_url":"https://github.com/sanger-tol/ascc","last_synced_at":"2025-09-01T23:06:59.110Z","status":null,"issues_count":38,"pull_requests_count":55,"avg_time_to_close_issue":9223317.19047619,"avg_time_to_close_pull_request":1336652.2702702703,"issues_closed_count":21,"pull_requests_closed_count":37,"pull_request_authors_count":5,"issue_authors_count":7,"avg_comments_per_issue":1.0263157894736843,"avg_comments_per_pull_request":1.2,"merged_pull_requests_count":31,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":25,"past_year_pull_requests_count":52,"past_year_avg_time_to_close_issue":3811720.076923077,"past_year_avg_time_to_close_pull_request":1062639.0,"past_year_issues_closed_count":13,"past_year_pull_requests_closed_count":35,"past_year_pull_request_authors_count":4,"past_year_issue_authors_count":4,"past_year_avg_comments_per_issue":0.96,"past_year_avg_comments_per_pull_request":1.2115384615384615,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":29,"created_at":"2025-08-29T11:54:07.840Z","updated_at":"2025-09-03T03:08:47.731Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fascc","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/sanger-tol%2Fascc/issues","issue_labels_count":{"enhancement":19,"bug":11,"Release 1":7},"pull_request_labels_count":{"enhancement":11,"Release 1":5,"documentation":4,"WIP":2,"1.X.X":1,"bug":1},"issue_author_associations_count":{"CONTRIBUTOR":38,"NONE":7},"pull_request_author_associations_count":{"CONTRIBUTOR":51,"NONE":5,"COLLABORATOR":4},"issue_authors":{"DLBPointon":33,"foreignsand":6,"eeaunin":3,"yumisims":1,"Surbhigrewal":1,"prototaxites":1},"pull_request_authors":{"DLBPointon":44,"eeaunin":8,"prototaxites":6,"sanger-tolsoft":1,"weaglesBio":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":11,"bug":8},"past_year_pull_request_labels_count":{"enhancement":10,"Release 1":5,"documentation":4,"WIP":2,"1.X.X":1,"bug":1},"past_year_issue_author_associations_count":{"CONTRIBUTOR":20,"NONE":7},"past_year_pull_request_author_associations_count":{"CONTRIBUTOR":45,"NONE":5,"COLLABORATOR":4},"past_year_issue_authors":{"DLBPointon":19,"foreignsand":6,"prototaxites":1,"Surbhigrewal":1},"past_year_pull_request_authors":{"DLBPointon":40,"eeaunin":7,"prototaxites":6,"sanger-tolsoft":1},"maintainers":[{"login":"eeaunin","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/eeaunin"}],"active_maintainers":[{"login":"eeaunin","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/eeaunin"}]},"events":{"total":{"ForkEvent":1,"CreateEvent":52,"CommitCommentEvent":3,"ReleaseEvent":3,"IssuesEvent":48,"WatchEvent":1,"DeleteEvent":34,"MemberEvent":1,"IssueCommentEvent":141,"PushEvent":394,"PullRequestReviewEvent":148,"PullRequestReviewCommentEvent":174,"PullRequestEvent":96},"last_year":{"ForkEvent":1,"CreateEvent":52,"CommitCommentEvent":3,"ReleaseEvent":3,"IssuesEvent":48,"WatchEvent":1,"DeleteEvent":34,"MemberEvent":1,"IssueCommentEvent":141,"PushEvent":394,"PullRequestReviewEvent":148,"PullRequestReviewCommentEvent":174,"PullRequestEvent":96}},"keywords":["genomics","nextflow","pipeline"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2023-10-03T07:59:20.171Z","updated_at":"2023-10-03T07:59:20.171Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/.github/workflows/branch.yml","dependencies":[{"id":14075727175,"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":"2023-10-03T07:59:21.181Z","updated_at":"2023-10-03T07:59:21.181Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/.github/workflows/ci.yml","dependencies":[{"id":14075727467,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":14075727468,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/clean-up.yml","sha":null,"kind":"manifest","created_at":"2023-10-03T07:59:21.543Z","updated_at":"2023-10-03T07:59:21.543Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/.github/workflows/clean-up.yml","dependencies":[{"id":14075727497,"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":"2023-10-03T07:59:21.622Z","updated_at":"2023-10-03T07:59:21.622Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/.github/workflows/fix-linting.yml","dependencies":[{"id":14075727505,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":14075727506,"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":"2023-10-03T07:59:21.730Z","updated_at":"2023-10-03T07:59:21.730Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/.github/workflows/linting.yml","dependencies":[{"id":14075727510,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":14075727511,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":14075727512,"package_name":"psf/black","ecosystem":"actions","requirements":"stable","direct":true,"kind":"composite","optional":false},{"id":14075727513,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":14075727514,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":14075727515,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":14075727516,"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":"2023-10-03T07:59:22.059Z","updated_at":"2023-10-03T07:59:22.059Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/.github/workflows/linting_comment.yml","dependencies":[{"id":14075728984,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":14075728985,"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":"2023-10-03T07:59:22.253Z","updated_at":"2023-10-03T07:59:22.253Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/custom/dumpsoftwareversions/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastqc/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-03T07:59:22.347Z","updated_at":"2023-10-03T07:59:22.347Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/kraken2/kraken2/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-03T07:59:22.418Z","updated_at":"2023-10-03T07:59:22.418Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/kraken2/kraken2/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-03T07:59:22.870Z","updated_at":"2023-10-03T07:59:22.870Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tiara/tiara/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-03T07:59:22.960Z","updated_at":"2023-10-03T07:59:22.960Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/tiara/tiara/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2023-10-03T07:59:23.734Z","updated_at":"2023-10-03T07:59:23.734Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/pyproject.toml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/blast/blastn/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.635Z","updated_at":"2023-10-11T12:10:27.635Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/blast/blastn/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/blast/makeblastdb/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.639Z","updated_at":"2023-10-11T12:10:27.639Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/blast/makeblastdb/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/custom/getchromsizes/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.645Z","updated_at":"2023-10-11T12:10:27.645Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/custom/getchromsizes/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/diamond/blastx/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.651Z","updated_at":"2023-10-11T12:10:27.651Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/diamond/blastx/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fcs/fcsadaptor/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.660Z","updated_at":"2023-10-11T12:10:27.660Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/fcs/fcsadaptor/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fcs/fcsgx/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.666Z","updated_at":"2023-10-11T12:10:27.666Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/fcs/fcsgx/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/gnu/sort/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.671Z","updated_at":"2023-10-11T12:10:27.671Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/gnu/sort/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/minimap2/align/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.679Z","updated_at":"2023-10-11T12:10:27.679Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/minimap2/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/minimap2/index/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.687Z","updated_at":"2023-10-11T12:10:27.687Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/minimap2/index/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/depth/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.705Z","updated_at":"2023-10-11T12:10:27.705Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/samtools/depth/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/faidx/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.710Z","updated_at":"2023-10-11T12:10:27.710Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/samtools/faidx/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/index/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.714Z","updated_at":"2023-10-11T12:10:27.714Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/samtools/index/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/sort/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.718Z","updated_at":"2023-10-11T12:10:27.718Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/samtools/sort/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/seqkit/sliding/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-11T12:10:27.722Z","updated_at":"2023-10-11T12:10:27.722Z","repository_link":"https://github.com/sanger-tol/ascc/blob/main/modules/nf-core/seqkit/sliding/meta.yml","dependencies":[]}],"score":null,"created_at":"2025-09-04T15:51:10.337Z","updated_at":"2025-10-07T08:15:09.261Z","avatar_url":"https://github.com/sanger-tol.png","language":"Python","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/36695","html_url":"https://science.ecosyste.ms/projects/36695","bibtex_url":"https://science.ecosyste.ms/projects/36695/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/36695/export.apalike"}