{"id":19857055,"url":"https://github.com/griffithlab/bioinformatic-workflows","last_synced_at":"2026-02-10T06:33:30.682Z","repository":{"id":78129547,"uuid":"147584103","full_name":"griffithlab/bioinformatic-workflows","owner":"griffithlab","description":"CWL workflows for bioinformatic analysis","archived":false,"fork":false,"pushed_at":"2019-08-16T21:19:30.000Z","size":72,"stargazers_count":1,"open_issues_count":1,"forks_count":3,"subscribers_count":16,"default_branch":"master","last_synced_at":"2025-08-22T13:42:19.783Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Common Workflow Language","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/griffithlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-09-05T21:58:21.000Z","updated_at":"2024-03-13T05:33:27.000Z","dependencies_parsed_at":"2023-02-24T02:00:49.315Z","dependency_job_id":null,"html_url":"https://github.com/griffithlab/bioinformatic-workflows","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/griffithlab/bioinformatic-workflows","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fbioinformatic-workflows","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fbioinformatic-workflows/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fbioinformatic-workflows/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fbioinformatic-workflows/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/griffithlab","download_url":"https://codeload.github.com/griffithlab/bioinformatic-workflows/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/griffithlab%2Fbioinformatic-workflows/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29292102,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-10T03:42:42.660Z","status":"ssl_error","status_checked_at":"2026-02-10T03:42:41.897Z","response_time":65,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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"}},"keywords":[],"created_at":"2024-11-12T14:17:21.241Z","updated_at":"2026-02-10T06:33:30.670Z","avatar_url":"https://github.com/griffithlab.png","language":"Common Workflow Language","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Description\n\nThis repository holds various bioinformatic workflows. Each workflow is broken down as a main or sub workflow and has an associated .yaml file specifying inputs and are named to correspond with the workflow they are associated with. A list of each available workflow is provided below, for a more complete description of a specific workflow see the [github wiki](https://github.com/griffithlab/bioinformatic-workflows/wiki).\n\n# Main Worfklows\n\n1. kallisto - Run kallisto from a bam file\n2. hla_typing - Run optitype and xHLA from a bam file\n2. hla_somatic_variants - Call somatic variants within the HLA region\n\n# Sub Workflows\n\n1. bam2fastq - Convert a paired end bam file to fastq files.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fbioinformatic-workflows","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgriffithlab%2Fbioinformatic-workflows","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgriffithlab%2Fbioinformatic-workflows/lists"}