{"id":23229018,"url":"https://github.com/common-workflow-language/workflow-service","last_synced_at":"2025-07-05T09:05:55.093Z","repository":{"id":4884056,"uuid":"42565850","full_name":"common-workflow-language/workflow-service","owner":"common-workflow-language","description":"Implementation of the GA4GH Workflow Execution Service, a REST service for running workflows","archived":false,"fork":false,"pushed_at":"2025-05-30T05:28:54.000Z","size":366,"stargazers_count":36,"open_issues_count":28,"forks_count":22,"subscribers_count":12,"default_branch":"main","last_synced_at":"2025-05-30T06:56:12.252Z","etag":null,"topics":["python"],"latest_commit_sha":null,"homepage":"","language":"Python","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/common-workflow-language.png","metadata":{"funding":{"custom":["https://www.commonwl.org/donate/","https://www.paypal.com/cgi-bin/webscr?cmd=_s-xclick\u0026hosted_button_id=Z55VS5LBBSZTJ"]},"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,"zenodo":null}},"created_at":"2015-09-16T05:06:55.000Z","updated_at":"2025-05-30T05:28:57.000Z","dependencies_parsed_at":"2025-05-01T09:19:13.420Z","dependency_job_id":"dfb6842d-e6d1-437d-94ab-2672c6b20dc2","html_url":"https://github.com/common-workflow-language/workflow-service","commit_stats":null,"previous_names":["common-workflow-language/cwltool-service"],"tags_count":11,"template":false,"template_full_name":null,"purl":"pkg:github/common-workflow-language/workflow-service","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/common-workflow-language%2Fworkflow-service","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/common-workflow-language%2Fworkflow-service/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/common-workflow-language%2Fworkflow-service/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/common-workflow-language%2Fworkflow-service/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/common-workflow-language","download_url":"https://codeload.github.com/common-workflow-language/workflow-service/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/common-workflow-language%2Fworkflow-service/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263715327,"owners_count":23500242,"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":["python"],"created_at":"2024-12-19T01:15:55.873Z","updated_at":"2025-07-05T09:05:55.086Z","avatar_url":"https://github.com/common-workflow-language.png","language":"Python","funding_links":["https://www.commonwl.org/donate/","https://www.paypal.com/cgi-bin/webscr?cmd=_s-xclick\u0026hosted_button_id=Z55VS5LBBSZTJ"],"categories":[],"sub_categories":[],"readme":"# Workflow as a Service\n\nThis is a client and server implementation of the [GA4GH Workflow\nExecution Service](https://github.com/ga4gh/workflow-execution-schemas) 1.0.0 API.\n\nIt provides [Arvados](https://arvados.org/) and [Toil](http://toil.ucsc-cgl.org/) backends.  It\nalso works with any `cwl-runner` that supports the CWL standard command line\ninterface: \u003chttp://www.commonwl.org/v1.0/CommandLineTool.html#Executing_CWL_documents_as_scripts\u003e\n\n## Installation:\n\n```\npip install wes-service\n```\n\n## Usage\n\n### Client configuration\n\nCommand line parameter or environment variable.\n\n`--host` or `WES_API_HOST`\n\nThe host to contact.\n\n`--proto` or `WES_API_PROTO`\n\nThe protocol (http or https) to use.\n\n`--auth` or `WES_API_AUTH`\n\nCredentials.  Format is 'Header: value' or just 'value'.  If header name is not provided, value goes in the 'Authorization'.\n\n### Get service info\n\n```\n$ wes-client --info\n```\n\n### Submit a workflow to run:\n\nAttachments must be accessible from the filesystem.  Workflow runners may also support http URLs or other storage systems.\n\n```\n$ wes-client --host localhost:8080 --proto http                             \\\n   --attachments=\"testdata/dockstore-tool-md5sum.cwl,testdata/md5sum.input\" \\\n   testdata/md5sum.cwl testdata/md5sum.cwl.json\n```\n\n### List workflows\n\n```\n$ wes-client --list\n```\n\n### Get workflow status\n\n```\n$ wes-client --get \u003crun-id\u003e\n```\n\n### Get stderr log from workflow:\n\n```\n$ wes-client --log \u003crun-id\u003e\n```\n\n## Server Configuration\n\n### Run a standalone server with default `cwl-runner` backend:\n\n```\n$ wes-server\n```\n\n### Run a standalone server with Arvados backend:\n\n```\n$ pip install arvados-cwl-runner\n$ wes-server --backend=wes_service.arvados_wes\n```\n\n### Run a standalone server with Toil backend:\n\n```\n$ pip install toil[all]\n$ wes-server --backend=wes_service.toil_wes --opt extra=--clean=never\n```\n\n### Use alternate executable with cwl-runner backend\n\n```\n$ pip install cwltool\n$ wes-server --backend=wes_service.cwl_runner --opt runner=cwltool --opt extra=--debug\n```\n\n### Pass parameters to cwl-runner\n\nUse \"--opt\" following by \"key=value\"\n\n```\n$ wes-server --backend=wes_service.cwl_runner --opt extra=--workDir=/tmp/work\n```\n\n## Development\nIf you would like to develop against `workflow-service` make sure you pass the provided test and it is flake8 compliant\n\n#### Install from Source\n\n```\n$ virtualenv venv \u0026\u0026 source venv/bin/activate \u0026\u0026 pip install toil[all] \u0026\u0026 pip install . --process-dependency-links \u0026\u0026 pip install -r dev-requirements.txt\n```\n\n#### Running Tests\nFrom path `workflow-service` run\n\n```\n$ pytest \u0026\u0026 flake8\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcommon-workflow-language%2Fworkflow-service","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcommon-workflow-language%2Fworkflow-service","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcommon-workflow-language%2Fworkflow-service/lists"}