{"id":21134228,"url":"https://github.com/cometsong/gbrs_nxf","last_synced_at":"2026-01-02T15:05:17.579Z","repository":{"id":141630390,"uuid":"312643193","full_name":"cometsong/gbrs_nxf","owner":"cometsong","description":"Analyze RNAseq with GBRS; Nextflow pipeline.","archived":false,"fork":false,"pushed_at":"2020-11-13T17:56:10.000Z","size":25,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-21T06:29:05.251Z","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":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cometsong.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2020-11-13T17:36:43.000Z","updated_at":"2020-11-13T17:56:14.000Z","dependencies_parsed_at":null,"dependency_job_id":"72627528-6b81-4ae1-9dda-d1e3112cf894","html_url":"https://github.com/cometsong/gbrs_nxf","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cometsong%2Fgbrs_nxf","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cometsong%2Fgbrs_nxf/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cometsong%2Fgbrs_nxf/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cometsong%2Fgbrs_nxf/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cometsong","download_url":"https://codeload.github.com/cometsong/gbrs_nxf/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243581060,"owners_count":20314162,"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":"2024-11-20T06:25:19.792Z","updated_at":"2026-01-02T15:05:17.562Z","avatar_url":"https://github.com/cometsong.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"Run GBRS (https://github.com/churchill-lab/gbrs) on paired-end RNAseq data using\nNextflow pipelines.\n\nThis is adapted to Sumner cluster (slurm, singularity) and uses the\njaxreg.jax.org containers repository, follow the User Guide there to add it to\nyour library.\n\nTo test it, install nextflow and run:\n```bash\nnextflow run TheJacksonLaboratory/gbrs_nxf -profile singularity,slurm \\\n  -resume --params-file \u003cparameter_yaml_file\u003e\n```\nMake sure the input files are in the format: `ID_*R{1,2}*.fastq.gz`\n\nThe parameter file is a `yaml` formatted file that contains at least the\nparameter entries:\n```yaml\nfastqR1: [path]\nfastqR2: [path]\noutputDir: [path]\ngeneration: '[G0-G40]'\nsex: [M|F]\n```\nPlus any other optional parameters, which can be shown by passing the `--help`\nargument i.e. `nextflow run TheJacksonLaboratory/gbrs_nxf --help`\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcometsong%2Fgbrs_nxf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcometsong%2Fgbrs_nxf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcometsong%2Fgbrs_nxf/lists"}