{"id":19749450,"url":"https://github.com/mskcc/tempo","last_synced_at":"2025-04-30T09:31:09.511Z","repository":{"id":38784713,"uuid":"166479564","full_name":"mskcc/tempo","owner":"mskcc","description":"CCS research pipeline to process WES and WGS TN pairs","archived":false,"fork":false,"pushed_at":"2024-11-07T16:13:27.000Z","size":31945,"stargazers_count":12,"open_issues_count":56,"forks_count":5,"subscribers_count":19,"default_branch":"master","last_synced_at":"2024-11-07T17:26:13.888Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://cmotempo.netlify.app/","language":"Groovy","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/mskcc.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"docs/contributing-to-tempo.md","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":"2019-01-18T22:18:51.000Z","updated_at":"2024-10-21T20:48:15.000Z","dependencies_parsed_at":"2024-04-24T19:29:06.785Z","dependency_job_id":"ed110914-c5b6-4404-b123-a1b739770042","html_url":"https://github.com/mskcc/tempo","commit_stats":null,"previous_names":[],"tags_count":42,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Ftempo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Ftempo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Ftempo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Ftempo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/tempo/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224204769,"owners_count":17273181,"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","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":"2024-11-12T02:26:32.156Z","updated_at":"2024-11-12T02:26:32.756Z","avatar_url":"https://github.com/mskcc.png","language":"Groovy","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build Status](https://travis-ci.com/mskcc/tempo.svg?token=DokCkCiDp43sqzeuXUHD\u0026branch=master)](https://travis-ci.com/mskcc/tempo)\n\n# \u003cimg id=\"logo\" src=\"./docs/tempoLogo.png\" height=\"42\" align=\"left\"/\u003e TEMPO\n\nTempo is a CMO Computational Sciences (CCS) research pipeline processing WES \u0026 WGS tumor-normal pairs using the [Nextflow framework](https://www.nextflow.io/). Currently the pipeline is composed of alignment and QC, and detection of both somatic alterations and germline variants. Users can begin with inputs of either paired-end FASTQs or BAMs, and process these via the command line. \n\nFor further details of how to begin processing data with Tempo, please view our [documentation](https://cmotempo.netlify.com/). For contributing to this project, please make a pull request as detailed [here](https://cmotempo.netlify.com/contributing-to-tempo.html).\n\nThe inspiration for this project derives from [Sarek](https://github.com/SciLifeLab/Sarek), developed at [SciLifeLab](https://github.com/SciLifeLab).\n\n## Pipeline Flowchart\n\u003cp align=\"center\"\u003e\n  \u003cimg id=\"diagram\" src=\"./docs/pipeline-flowchart.png\"/\u003e\n\u003c/p\u003e\n\n## Directed Acyclic Graph\n\u003cp align=\"center\"\u003e\n  \u003cimg id=\"dag\" src=\"./docs/dag.png\"/\u003e\n\u003c/p\u003e\n\n##\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"./docs/brandenburg5_allegro.jpg\"\u003e\n\u003c/p\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Ftempo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Ftempo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Ftempo/lists"}