{"id":26359504,"url":"https://github.com/karchinlab/tcrtoolkit-bulk","last_synced_at":"2025-07-26T13:34:36.644Z","repository":{"id":240400458,"uuid":"802529681","full_name":"KarchinLab/TCRtoolkit-Bulk","owner":"KarchinLab","description":"A NextFlow pipeline for processing and analyzing TCRseq data","archived":false,"fork":false,"pushed_at":"2025-07-23T18:50:16.000Z","size":10815,"stargazers_count":1,"open_issues_count":16,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-07-23T20:48:26.859Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Nextflow","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/KarchinLab.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,"zenodo":null}},"created_at":"2024-05-18T14:52:49.000Z","updated_at":"2025-07-23T18:50:21.000Z","dependencies_parsed_at":"2025-07-23T20:29:00.914Z","dependency_job_id":null,"html_url":"https://github.com/KarchinLab/TCRtoolkit-Bulk","commit_stats":null,"previous_names":["karchinlab/tcrtoolkit-bulk"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/KarchinLab/TCRtoolkit-Bulk","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarchinLab%2FTCRtoolkit-Bulk","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarchinLab%2FTCRtoolkit-Bulk/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarchinLab%2FTCRtoolkit-Bulk/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarchinLab%2FTCRtoolkit-Bulk/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KarchinLab","download_url":"https://codeload.github.com/KarchinLab/TCRtoolkit-Bulk/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarchinLab%2FTCRtoolkit-Bulk/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267175154,"owners_count":24047773,"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":"2025-07-26T02:00:08.937Z","response_time":62,"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"}},"keywords":[],"created_at":"2025-03-16T15:59:57.062Z","updated_at":"2025-07-26T13:34:36.628Z","avatar_url":"https://github.com/KarchinLab.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# TCRtoolkit-Bulk: A T Cell Repertoire Analysis Platform\n\n![TCRtoolkit-banner](./assets/images/TCRtoolkit-banner.png)\n\nThanks for checking out `TCRtoolkit-Bulk`, the platform for bulk T Cell Repertoire analysis! `TCRtoolkit-Bulk` is wrapped in NextFlow, written in python, and uses Docker to manage dependencies.\n\n\u003cp align=\"center\"\u003e\n    \u003cimg src=assets/TCR_Bulk_profiling.png/\u003e\n\u003c/p\u003e\n\nWe currently support bulk TCRseq data from Adaptive Biotechnologies.\n\n##  Requirements\n\n1. Nextflow\n\nNextflow can be used on any POSIX-compatible system (Linux, OS X, WSL). It requires Bash 3.2 (or later) and Java 11 (or later, up to 18) to be installed.\n\n```{bash}\nwget -qO- https://get.nextflow.io | bash\nchmod +x nextflow\n```\n\nThe nextflow executable is now available to run on the command line. The executable can be moved to a directory in your $PATH variable so you can run it from any directory.\n\n2. Docker\n\n`TCRtoolkit-Bulk` runs in Docker containers available [here](https://hub.docker.com/repository/docker/karchinlab/bulktcr/general). Depending on what operating system you are running (Linux, MacOS, WSL), please refer to the [Docker documentation](https://docs.docker.com/engine/install/) for installation instructions.\n\n3. TCRtoolkit-Bulk\n\n```{bash}\ngit clone https://github.com/KarchinLab/TCRtoolkit-Bulk.git\ncd TCRtoolkit-Bulk\n```\n\n\n## Quick Start\n\nBelow is a minimal example of how to run the pipeline. The `minimal-example` dataset provided is a small subset of the dataset from this manuscript by [Tumeh and Ribas et al. (2014)](https://www.nature.com/articles/nature13954). Note that the results are simply for demonstration purposes and are not intended for biological interpretation.\n\n```\n## from the TCRtoolkit-Bulk directory\nnextflow run main.nf \\\n    --samplesheet test_data/minimal-example/samplesheet.csv \\\n    --outdir out-minimal-dev \\\n    --input_format adaptive \\\n    --max_memory 10GB --max_cpus 4\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarchinlab%2Ftcrtoolkit-bulk","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkarchinlab%2Ftcrtoolkit-bulk","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarchinlab%2Ftcrtoolkit-bulk/lists"}