{"id":19749593,"url":"https://github.com/mskcc/roslin-cwl","last_synced_at":"2026-03-06T04:03:52.178Z","repository":{"id":72596973,"uuid":"210447301","full_name":"mskcc/roslin-cwl","owner":"mskcc","description":"CWLs for the Roslin Variant Pipeline","archived":false,"fork":false,"pushed_at":"2020-05-13T15:27:29.000Z","size":313,"stargazers_count":0,"open_issues_count":6,"forks_count":1,"subscribers_count":12,"default_branch":"master","last_synced_at":"2025-05-12T21:49:40.533Z","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/mskcc.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":"2019-09-23T20:34:29.000Z","updated_at":"2020-05-13T15:26:57.000Z","dependencies_parsed_at":null,"dependency_job_id":"345ac2ff-e1d8-44be-9f47-e3f89d7b0aaf","html_url":"https://github.com/mskcc/roslin-cwl","commit_stats":null,"previous_names":[],"tags_count":11,"template":false,"template_full_name":null,"purl":"pkg:github/mskcc/roslin-cwl","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-cwl","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-cwl/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-cwl/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-cwl/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mskcc","download_url":"https://codeload.github.com/mskcc/roslin-cwl/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mskcc%2Froslin-cwl/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30161345,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-05T22:39:40.138Z","status":"online","status_checked_at":"2026-03-06T02:00:08.268Z","response_time":250,"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":"2024-11-12T02:27:21.693Z","updated_at":"2026-03-06T04:03:52.156Z","avatar_url":"https://github.com/mskcc.png","language":"Common Workflow Language","funding_links":[],"categories":[],"sub_categories":[],"readme":"# roslin-cwl\n\nCWLs for the Roslin pipeline.\n\nThe CWLs are categorized in multiple directories based on their unit of work, although the CWLs contained within can refer to other CWL directories via their relative path.\n\nFor example, each CWL module that performs at the tumor-normal pair level are contained in the `modules/pair` directory; workflows that perform executions by chaining multiple modules are contained in the `workflows` directory. The CWLs in `workflows/` will reference CWLs in `modules/pair/` to perform their tasks, such as `alignment-pair.cwl` and `variant-calling.cwl`.\n\n## Set up\n\nThis repo contains git submodules; make sure to `git clone --recursive` when downloading.\n\nCWLs have been tested with the `toil` executor, found [here](https://github.com/DataBiosphere/toil). \n\n## Directories\n\n#### modules/\n\nModule CWLs perform small pipeline operations to do a particular task. For example, `modules/pair/alignment.cwl` will takes a pair of tumor-normal samples and  align it with `bwa mem`, followed by `modules/pair/realignment.cwl`; this then returns a pair of tumor-normal bam files and some metrics.\n\nMultiple CWLs in this directory will refer to other CWLs in the `workflows/` and `tools/` directories.\n\n#### tools/\n\nContains CWLs for tools (`bwa`, `bcftools`, etc.) used by the modules and workflows.\n\n#### workflows/\n\nWorkflow CWLs that operate at either a sample level or at one paired tumor-normal level. Multiple CWLs in this directory will refer to other CWLs in the `modules/` and `tools/` directories.\n\n## CWLs\n\nThe two CWLs listed here expect input as a list of paired tumor-normal samples.\n\n#### project-workflow.cwl\n\nGiven a list of paired tumor-normal samples, this CWL uses `workflows/pair-workflow.cwl` to do alignment, variant calling, and some metrics, followed by `modules/project/generate-qc.cwl` to compile QC data.\n\n#### project-workflow-sv.cwl\n\nSimilar to `project-workflow.cwl`, given a list of paired tumor-normal samples, this CWL uses `workflows/pair-workflow-sv.cwl` to do alignment, variant calling (including structural variants), and some metrics, followed by `modules/project/generate-qc.cwl` to compile QC data for all tumor-normal pairs.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Froslin-cwl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Froslin-cwl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Froslin-cwl/lists"}