{"id":51403932,"url":"https://github.com/twlab/cig-pipelines","last_synced_at":"2026-07-04T09:32:33.625Z","repository":{"id":273834762,"uuid":"789148951","full_name":"twlab/cig-pipelines","owner":"twlab","description":null,"archived":false,"fork":false,"pushed_at":"2026-06-23T22:40:15.000Z","size":555,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2026-06-24T00:21:43.569Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"WDL","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/twlab.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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-04-19T19:52:17.000Z","updated_at":"2026-06-23T22:40:19.000Z","dependencies_parsed_at":"2025-01-23T08:55:17.035Z","dependency_job_id":"cbd2408e-fa4d-449b-bac3-348d105bcbbb","html_url":"https://github.com/twlab/cig-pipelines","commit_stats":null,"previous_names":["twlab/cig-pipelines"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/twlab/cig-pipelines","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/twlab%2Fcig-pipelines","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/twlab%2Fcig-pipelines/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/twlab%2Fcig-pipelines/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/twlab%2Fcig-pipelines/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/twlab","download_url":"https://codeload.github.com/twlab/cig-pipelines/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/twlab%2Fcig-pipelines/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35117335,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-04T02:00:05.987Z","response_time":113,"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":"2026-07-04T09:32:33.001Z","updated_at":"2026-07-04T09:32:33.617Z","avatar_url":"https://github.com/twlab.png","language":"WDL","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CIG@MGI Pipelines\n\nThe Collaborative and Intergrative Genomics (CIG) is a group in the [McDonnell Genome Institute](https://www.genome.wustl.edu/) (MGI) at the [Washington University School of Medicine](https://medicine.wustl.edu/) (WUSM).\n\n## Overview\n\nIn this repo, we share genomics pipelines, tools, and tasks, mostly in the form of [WDL](https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md). Corresponding Dockerfiles and scripts are at [CIG Containters](https://github.com/twlab/cig-containers).\n\n## Repo Structure\n\n| Path          | Description |\n| ---           | --- |\n| scripts       | helpers scripts for pipelines; these are not used in pipelines/tools |\n| wdl/pipelines | full start to end workflows that produce outputs from many tasks |\n| wdl/tasks     | wrapped command line interfaces and scripts (must be incorporated into tools/pipelines) |\n| wdl/tools     | stand alone workflows that combine a few tasks to produce outputs |\n| wdl/structs   | data structures and types for pipelines, tools, and tasks |\n\n# Building WDL Imports\nWDLs have imports that bring in functionality from other WDL files. When running **cromwell**, a zip file of the imports is required. These WDL imports ZIP files are not included in the repo, but can be easily built with the *build_imports* script. From the main directory run the *build_imports* script giving the WDL file as the sole input. The output will be next to the WDL, named with the basename of the WDL file with the extension *.wdl* replaced with *.imports.zip*. Here is an example building the imports for *wdl/tools/pacbio/align_output_cram.wdl*:\n\n```\n$ cd cig-pipelines\n$ bash ./scripts/build_imports wdl/tools/pacbio/align_output_cram.wdl \nWDL: wdl/tools/pacbio/align_output_cram.wdl\nArchive:  align_output_cram.imports.zip\n  Length      Date    Time    Name\n---------  ---------- -----   ----\n        0  2025-08-13 14:14   wdl/\n        0  2025-08-13 14:14   wdl/structs/\n      285  2025-08-13 14:14   wdl/structs/runenv.wdl\n        0  2025-08-13 14:14   wdl/tasks/\n        0  2025-08-13 14:14   wdl/tasks/pacbio/\n     1568  2025-08-13 14:14   wdl/tasks/pacbio/pbmm2.wdl\n---------                     -------\n     1853                     6 files\nCreated imports file: wdl/tools/pacbio/align_output_cram.imports.zip\n\n```\n\nThe *tools* and *pipelines* imports include the absolute paths of import WDL files. The *tasks* imports, which are typically limited, include the relative path of the imports. Pipeline and tool WDLs can use task WDLs, and task WDLs should only use other task WDLs.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftwlab%2Fcig-pipelines","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftwlab%2Fcig-pipelines","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftwlab%2Fcig-pipelines/lists"}