{"id":46041,"name":"xavier","description":"An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH","url":"https://github.com/ccbr/xavier","last_synced_at":"2025-09-05T10:40:39.137Z","repository":{"id":37808464,"uuid":"506288958","full_name":"CCBR/XAVIER","owner":"CCBR","description":"An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH","archived":false,"fork":false,"pushed_at":"2025-07-15T20:43:14.000Z","size":65803,"stargazers_count":6,"open_issues_count":11,"forks_count":3,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-07-16T18:50:18.531Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://ccbr.github.io/XAVIER/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"mtandon09/CCBR_GATK4_Exome_Seq_Pipeline","license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/CCBR.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":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-06-22T14:46:39.000Z","updated_at":"2025-07-15T20:42:21.000Z","dependencies_parsed_at":"2023-07-14T23:39:58.466Z","dependency_job_id":"61416b60-4727-4c2c-97bc-6a635636a7c4","html_url":"https://github.com/CCBR/XAVIER","commit_stats":null,"previous_names":["ccbr/xavier"],"tags_count":15,"template":false,"template_full_name":null,"purl":"pkg:github/CCBR/XAVIER","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CCBR%2FXAVIER","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CCBR%2FXAVIER/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CCBR%2FXAVIER/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CCBR%2FXAVIER/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CCBR","download_url":"https://codeload.github.com/CCBR/XAVIER/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CCBR%2FXAVIER/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273747216,"owners_count":25160649,"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":"CCBR","name":"CCR Collaborative Bioinformatics Resource","uuid":"10426639","kind":"organization","description":"CCR Collaborative Bioinformatics Resource, Center for Cancer Research (NCI), National Institutes of Health","email":"nciccbr@mail.nih.gov","website":"https://bioinformatics.ccr.cancer.gov/ccbr/","location":"United States of America","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/10426639?v=4","repositories_count":92,"last_synced_at":"2024-04-19T04:44:18.139Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/CCBR","funding_links":[],"total_stars":85,"followers":30,"following":0,"created_at":"2022-11-12T07:35:16.356Z","updated_at":"2024-04-19T04:44:52.738Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CCBR","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CCBR/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"CCBR/XAVIER","html_url":"https://github.com/CCBR/XAVIER","last_synced_at":"2025-08-31T13:18:28.000Z","status":null,"issues_count":13,"pull_requests_count":27,"avg_time_to_close_issue":1585201.6666666667,"avg_time_to_close_pull_request":476608.04,"issues_closed_count":6,"pull_requests_closed_count":25,"pull_request_authors_count":5,"issue_authors_count":5,"avg_comments_per_issue":0.3076923076923077,"avg_comments_per_pull_request":0.037037037037037035,"merged_pull_requests_count":23,"bot_issues_count":1,"bot_pull_requests_count":10,"past_year_issues_count":13,"past_year_pull_requests_count":27,"past_year_avg_time_to_close_issue":1585201.6666666667,"past_year_avg_time_to_close_pull_request":476608.04,"past_year_issues_closed_count":6,"past_year_pull_requests_closed_count":25,"past_year_pull_request_authors_count":5,"past_year_issue_authors_count":5,"past_year_avg_comments_per_issue":0.3076923076923077,"past_year_avg_comments_per_pull_request":0.037037037037037035,"past_year_bot_issues_count":1,"past_year_bot_pull_requests_count":10,"past_year_merged_pull_requests_count":23,"created_at":"2025-07-16T12:49:38.106Z","updated_at":"2025-09-03T00:38:43.056Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/CCBR%2FXAVIER","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/CCBR%2FXAVIER/issues","issue_labels_count":{"bug":6,"documentation":2,"ccbrpipeliner/7":2,"high priority":1,"enhancement":1},"pull_request_labels_count":{"dependencies":4,"python":4,"enhancement":1,"bug":1},"issue_author_associations_count":{"MEMBER":19,"COLLABORATOR":11,"CONTRIBUTOR":4,"NONE":1},"pull_request_author_associations_count":{"MEMBER":36,"COLLABORATOR":15,"CONTRIBUTOR":14,"NONE":2},"issue_authors":{"kelly-sovacool":15,"samarth8392":14,"kopardev":3,"dnousome":2,"VidhurDS":1},"pull_request_authors":{"kelly-sovacool":34,"samarth8392":16,"github-actions[bot]":8,"dnousome":4,"dependabot[bot]":4,"kopardev":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10097364,"issues_count":31428117,"pull_requests_count":97242359,"authors_count":10701128,"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":2},"past_year_pull_request_labels_count":{"dependencies":4,"python":4,"bug":1},"past_year_issue_author_associations_count":{"MEMBER":6,"COLLABORATOR":5,"CONTRIBUTOR":4,"NONE":1},"past_year_pull_request_author_associations_count":{"MEMBER":16,"CONTRIBUTOR":13,"COLLABORATOR":5,"NONE":2},"past_year_issue_authors":{"samarth8392":9,"kelly-sovacool":5,"dnousome":1,"VidhurDS":1},"past_year_pull_request_authors":{"kelly-sovacool":15,"samarth8392":9,"github-actions[bot]":7,"dependabot[bot]":4,"dnousome":1},"maintainers":[{"login":"kelly-sovacool","count":49,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/kelly-sovacool"},{"login":"samarth8392","count":22,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/samarth8392"},{"login":"dnousome","count":6,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/dnousome"},{"login":"kopardev","count":4,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/kopardev"}],"active_maintainers":[{"login":"kelly-sovacool","count":20,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/kelly-sovacool"},{"login":"samarth8392","count":10,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/samarth8392"},{"login":"dnousome","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/dnousome"}]},"events":{"total":{"CreateEvent":37,"ReleaseEvent":5,"IssuesEvent":25,"WatchEvent":5,"DeleteEvent":30,"MemberEvent":1,"IssueCommentEvent":20,"PushEvent":78,"PullRequestReviewCommentEvent":8,"PullRequestReviewEvent":22,"PullRequestEvent":55},"last_year":{"CreateEvent":37,"ReleaseEvent":5,"IssuesEvent":25,"WatchEvent":5,"DeleteEvent":30,"MemberEvent":1,"IssueCommentEvent":20,"PushEvent":78,"PullRequestReviewCommentEvent":8,"PullRequestReviewEvent":22,"PullRequestEvent":55}},"keywords":[],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/docs.yml","sha":null,"kind":"manifest","created_at":"2023-02-12T04:01:33.043Z","updated_at":"2023-02-12T04:01:33.043Z","repository_link":"https://github.com/CCBR/XAVIER/blob/main/.github/workflows/docs.yml","dependencies":[{"id":7569393059,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7569393062,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/main.yaml","sha":null,"kind":"manifest","created_at":"2023-02-12T04:01:33.094Z","updated_at":"2023-02-12T04:01:33.094Z","repository_link":"https://github.com/CCBR/XAVIER/blob/main/.github/workflows/main.yaml","dependencies":[{"id":7569393228,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":7569393229,"package_name":"docker://snakemake/snakemake","ecosystem":"actions","requirements":"v5.24.2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"docker","filepath":"docker/mutect/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-02-12T04:01:33.190Z","updated_at":"2023-02-12T04:01:33.190Z","repository_link":"https://github.com/CCBR/XAVIER/blob/main/docker/mutect/Dockerfile","dependencies":[{"id":7569393299,"package_name":"ubuntu","ecosystem":"docker","requirements":"14.04","direct":true,"kind":"build","optional":false}]},{"ecosystem":"docker","filepath":"docker/vcf2maf/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-02-12T04:01:33.211Z","updated_at":"2023-02-12T04:01:33.211Z","repository_link":"https://github.com/CCBR/XAVIER/blob/main/docker/vcf2maf/Dockerfile","dependencies":[{"id":7569393845,"package_name":"ensemblorg/ensembl-vep","ecosystem":"docker","requirements":"release_102.0","direct":true,"kind":"build","optional":false}]},{"ecosystem":"docker","filepath":"docker/wes_base/Dockerfile","sha":null,"kind":"manifest","created_at":"2023-02-12T04:01:33.244Z","updated_at":"2023-02-12T04:01:33.244Z","repository_link":"https://github.com/CCBR/XAVIER/blob/main/docker/wes_base/Dockerfile","dependencies":[{"id":7569393851,"package_name":"ubuntu","ecosystem":"docker","requirements":"20.04","direct":true,"kind":"build","optional":false}]},{"ecosystem":"pypi","filepath":"docs/requirements.txt","sha":null,"kind":"manifest","created_at":"2023-02-12T04:01:33.271Z","updated_at":"2023-02-12T04:01:33.271Z","repository_link":"https://github.com/CCBR/XAVIER/blob/main/docs/requirements.txt","dependencies":[{"id":7569393858,"package_name":"Babel","ecosystem":"pypi","requirements":"==2.8.0","direct":true,"kind":"runtime","optional":false},{"id":7569393859,"package_name":"click","ecosystem":"pypi","requirements":"==7.1.2","direct":true,"kind":"runtime","optional":false},{"id":7569393860,"package_name":"future","ecosystem":"pypi","requirements":"==0.18.2","direct":true,"kind":"runtime","optional":false},{"id":7569393861,"package_name":"gitdb","ecosystem":"pypi","requirements":"==4.0.5","direct":true,"kind":"runtime","optional":false},{"id":7569393862,"package_name":"GitPython","ecosystem":"pypi","requirements":"==3.1.7","direct":true,"kind":"runtime","optional":false},{"id":7569393863,"package_name":"htmlmin","ecosystem":"pypi","requirements":"==0.1.12","direct":true,"kind":"runtime","optional":false},{"id":7569393864,"package_name":"importlib-metadata","ecosystem":"pypi","requirements":"==1.7.0","direct":true,"kind":"runtime","optional":false},{"id":7569393865,"package_name":"Jinja2","ecosystem":"pypi","requirements":"==2.11.2","direct":true,"kind":"runtime","optional":false},{"id":7569393866,"package_name":"joblib","ecosystem":"pypi","requirements":"==0.16.0","direct":true,"kind":"runtime","optional":false},{"id":7569393867,"package_name":"jsmin","ecosystem":"pypi","requirements":"==3.0.0","direct":true,"kind":"runtime","optional":false},{"id":7569393868,"package_name":"livereload","ecosystem":"pypi","requirements":"==2.6.1","direct":true,"kind":"runtime","optional":false},{"id":7569393869,"package_name":"lunr","ecosystem":"pypi","requirements":"==0.5.8","direct":true,"kind":"runtime","optional":false},{"id":7569393870,"package_name":"Markdown","ecosystem":"pypi","requirements":"==3.2.2","direct":true,"kind":"runtime","optional":false},{"id":7569393871,"package_name":"MarkupSafe","ecosystem":"pypi","requirements":"==1.1.1","direct":true,"kind":"runtime","optional":false},{"id":7569393872,"package_name":"mkdocs","ecosystem":"pypi","requirements":"==1.1.2","direct":true,"kind":"runtime","optional":false},{"id":7569393873,"package_name":"mkdocs-awesome-pages-plugin","ecosystem":"pypi","requirements":"==2.2.1","direct":true,"kind":"runtime","optional":false},{"id":7569393874,"package_name":"mkdocs-git-revision-date-localized-plugin","ecosystem":"pypi","requirements":"==0.7","direct":true,"kind":"runtime","optional":false},{"id":7569393875,"package_name":"mkdocs-material","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":7569393876,"package_name":"mkdocs-material-extensions","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":7569393877,"package_name":"mkdocs-minify-plugin","ecosystem":"pypi","requirements":"==0.3.0","direct":true,"kind":"runtime","optional":false},{"id":7569393878,"package_name":"mkdocs-redirects","ecosystem":"pypi","requirements":"==1.0.1","direct":true,"kind":"runtime","optional":false},{"id":7569393879,"package_name":"nltk","ecosystem":"pypi","requirements":"==3.5","direct":true,"kind":"runtime","optional":false},{"id":7569393880,"package_name":"Pygments","ecosystem":"pypi","requirements":"==2.6.1","direct":true,"kind":"runtime","optional":false},{"id":7569393881,"package_name":"pymdown-extensions","ecosystem":"pypi","requirements":"==7.1","direct":true,"kind":"runtime","optional":false},{"id":7569393882,"package_name":"pytz","ecosystem":"pypi","requirements":"==2020.1","direct":true,"kind":"runtime","optional":false},{"id":7569393883,"package_name":"PyYAML","ecosystem":"pypi","requirements":"==5.3.1","direct":true,"kind":"runtime","optional":false},{"id":7569393884,"package_name":"regex","ecosystem":"pypi","requirements":"==2020.7.14","direct":true,"kind":"runtime","optional":false},{"id":7569393885,"package_name":"six","ecosystem":"pypi","requirements":"==1.15.0","direct":true,"kind":"runtime","optional":false},{"id":7569393886,"package_name":"smmap","ecosystem":"pypi","requirements":"==3.0.4","direct":true,"kind":"runtime","optional":false},{"id":7569393887,"package_name":"tornado","ecosystem":"pypi","requirements":"==6.0.4","direct":true,"kind":"runtime","optional":false},{"id":7569393888,"package_name":"tqdm","ecosystem":"pypi","requirements":"==4.48.2","direct":true,"kind":"runtime","optional":false},{"id":7569393889,"package_name":"zipp","ecosystem":"pypi","requirements":"==3.1.0","direct":true,"kind":"runtime","optional":false},{"id":7569393890,"package_name":"mkdocs-git-revision-date-plugin","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":7569393891,"package_name":"mike","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/forksync.yml","sha":null,"kind":"manifest","created_at":"2023-07-14T23:39:56.652Z","updated_at":"2023-07-14T23:39:56.652Z","repository_link":"https://github.com/CCBR/XAVIER/blob/main/.github/workflows/forksync.yml","dependencies":[{"id":11484192299,"package_name":"tgymnich/fork-sync","ecosystem":"actions","requirements":"v1.2.1","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/main.yml","sha":null,"kind":"manifest","created_at":"2023-07-14T23:39:57.353Z","updated_at":"2023-07-14T23:39:57.353Z","repository_link":"https://github.com/CCBR/XAVIER/blob/main/.github/workflows/main.yml","dependencies":[{"id":11484193942,"package_name":"tgymnich/fork-sync","ecosystem":"actions","requirements":"v1.2.1","direct":true,"kind":"composite","optional":false}]}],"score":null,"created_at":"2025-09-04T15:51:21.497Z","updated_at":"2025-10-07T08:18:23.751Z","avatar_url":"https://github.com/CCBR.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.12727315"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/46041","html_url":"https://science.ecosyste.ms/projects/46041"}