通用工作流语言(CWL)是一个开放的标准，用于描述、分析工作流和工具，使流程文件能够在各种软件和硬件环境(从工作站到集群、云和高性能计算(HPC)环境)中可移植和扩展。CWL旨在满足数据密集型科学的需求，如生物信息学、医学成像、天文学、高能物理和机器学习。
CWL是由一个由组织和个人组成的多工作组开发的，旨在让科学家共享数据分析工作流程。CWL项目在Github上维护，我们遵循协作开放标准开发的openstand.org原则。合法CWL属于工程软件自由保护协会,日常项目决策是由(CWL社区)(https://github.com/common-workflow-language/cwl-website/blob/main/README.md)支持开放参与的任何人。
开始
CWL用户指南提供了学习如何编写CWL命令行工具和工作流描述的温和介绍。
浏览CWL Implementations，找到适合你的软件包。
( CWL推荐实践 )(http://www.commonwl.org/user_guide/rec-practices/)
支持、社区和贡献
关于CWL的所有问题，建议在CWL话语组上提问。以前我们使用biostars.org，在那里你仍然可以阅读旧的回复。
如果你有兴趣学习更多或贡献想法或代码,(来和我们聊天在git) (https://gitter.im/common-workflow-language/common-workflow-language),检查(在Twitter上# CommonWL) (https://twitter.com/search?q=%23CommonWL),加入(邮件列表对谷歌集团common-workflow-language) (https://groups.google.com/forum/ !论坛/ common-workflow-language)或存储库(https://github.com/common-workflow-language/common-workflow-language)和发送拉请求!
除了邮件列表的web界面，用户还可以通过发送空白邮件到common-workflow-language+subscribe@googlegroups.com并回复自动回复来加入。
行为准则
CWL项目致力于为每个人提供无骚扰的体验，无论性别、性别认同和表达、性取向、残疾、外貌、体型、年龄、种族或宗教。我们不会容忍任何形式的骚扰参与者。本行为准则适用于所有CWL项目空间，包括在线和离线的谷歌组、Gitter聊天室、谷歌Hangouts聊天室。任何违反本行为准则的人，在领导团队的酌情决定下，将被处罚或驱逐出这些空间。
欲了解更多细节，请参见我们的行为准则。
规范
对于开发人员和高级用户，当前的CWL标准v1.2.0提供了执行CWL文档的权威文档。以前的版本CWL Standards v1.0.2和CWL Standards v1.1.0也可以使用。
引用
在学术著作中引用CWL标准，请使用以下引文(包括DOI):
Peter Amstutz, Michael R. Crusoe, Nebojša Tijanić (editors), Brad Chapman, John Chilton, Michael Heuer, Andrey Kartashov, Dan Leehr, Hervé Ménager, Maya Nedeljkovich, Matt Scales, Stian Soiland-Reyes, Luka Stojanovic (2016): Common Workflow Language, v1.0. Specification, Common Workflow Language working group. https://w3id.org/cwl/v1.0/ doi:10.6084/m9.figshare.3115156.v2
有关CWL的现有参考资料可于[https://zotero.org/groups/cwl]
实现
用于生产系统
| 软件 | 描述 | 平台支持 |
|---|---|---|
| cwltool | CWL的实现 | Linux, OS X, Windows, 仅本地化运行 |
| Arvados | 面向海量数据集数据分析的分布式计算平台. Using CWL on Arvados | 在云AWS、Azure、GCP，以及使用Slurm的混合集群 |
| Toil | Toil 是一个完全用Python编写的工作流引擎 toil-cwl-runner guide. | AWS, Azure, GCP, Grid Engine, HTCondor, LSF, Mesos, OpenStack, Slurm, PBS/Torque |
| CWL-Airflow | 在apache -airflow中运行CWL工作流程的包(由BioWardrobe Team, CCHMC支持) | Linux, OS X |
| REANA | RE usable ANAlyses | Kubernetes, CERN OpenStack (OpenStack Magnum) |
部分功能
| Software | Description | Platform support |
|---|---|---|
| Galaxy | Web-based platform for data intensive biomedical research. | Partial support for importing CWL tools and workflows is under development |
| cwl-tes | CWL engine backended by the GA4GH Task Execution API | Alicloud, AWS, Google, HPC, Local, Spark, TES |
| Xenon | Run CWL workflows using Xenon | any Xenon backend: local, ssh, SLURM, Torque, Grid Engine |
| Consonance | orchestration tool for running SeqWare workflows and CWL tools | AWS, OpenStack, Azure |
| AWE | Workflow and resource management system for bioinformatics data analysis. | - |
| yacle | Yet Another CWL Engine | local |
| Calrissian | CWL Engine built for Kubernetes | |
| Cromwell | Cromwell workflow engine | Google, HTCondor, Local, LSF, PBS/Torque, SGE, Slurm, TES |
| CWLEXEC | Apache 2.0 licensed CWL executor for IBM Spectrum LSF, supported by IBM for customers with valid contracts. | IBM Spectrum LSF 10.1.0.3+ |
| Mariner | “The Gen3 Workflow Execution Service”, Apache 2.0 licensed, written in Go, also implements the GA4GH WES API | Kubernetes |
| ep3 | Extremely Pluggable Pipeline Processor | local |
| Pegasus | Pegasus Workflow Management System | Partial support for importing CWL workflows is under development |
CWL工具和工作流的仓库
| Repository | Description |
|---|---|
| Common Workflow Library | Git organization for community maintenance of tools and workflows. |
| Dockstore tool registry | An open platform for sharing Docker-based tools described with the Common Workflow Language used by the GA4GH. |
| CWLviewer | A web application to view and share Common Workflow Language workflows |
| cwl-source | Git repository for collections of tools, workflows, metadata, and input parameter files. Administered by xD Bio Inc. Integrates with truwl.com |
| GitHub | Search for CWL documents using extension:cwl cwlVersion + <your search terms>, for example extension:cwl cwlVersion picard. |
Search for CWL documents using filetype:cwl cwlVersion + <your search terms>, for example filetype:cwl cwlVersion picard. |
|
| Workflow Hub | A registry for scientific workflows, sponsored by EOSC Life |
使用CWL的软件
编辑查看工具
| Software | Description |
|---|---|
| Rabix Composer | Graphical CWL editor |
| CWLviewer | A web application to view and share Common Workflow Language workflows |
| atom-cwl | CWL editing mode for Atom |
| vim-cwl | CWL editing mode for Vim |
| cwl-mode | CWL editing mode for Emacs (instructions english, 日本語) |
| vscode-cwl | CWL support in Visual Studio Code |
| IntelliJ CWL plugin | CWL plugin for IntelliJ and other JetBrains editors |
| bioSyntax | Includes CWL syntax highliting for gedit |
| Rabix Benten | A language server for CWL. Provides CWL code intelligence for VS Code, vim/neovim, Emacs, Acme, IntelliJ/JetBrains, and others |
| vue-cwl | Visualizer of CWL workflows for the Vue JavaScript framework using cwl-svg |
| cwl-for-remote-container-template | A template to write CWL documents with VSCode with remote container extension |
实用工具
| Software | Description |
|---|---|
| cwldep | CWL dependency manager, for importing tool wrappers and workflows into your own project. |
| cwltest | CWL testing framework, automated testing of tools and workflows written with CWL |
| cwl2zshcomp | generates ZSH auto completions from CWL command line tool descriptions |
| Cerise | A REST service for running CWL workflows on remote clusters |
| workflow-service | An implementation of the GA4GH Workflow Execution Service (WES) API to run CWL workflows on remote clusters |
| cwl-inspector | Tool to inspect properties of tools or workflows written in CWL |
| cwlprov-py | Command line tool and Python API to explore CWLProv Research Objects containing provenance of Common Workflow Language executions |
| cwl-utils | Example scripts using the new Python 3.6+ CWL parsing library, includes a script to cache all software containers for a given CWL document. |
| looper | job submitting engine with support for [CWL whole workflow/tool scattering]( |
转换器和代码生成器
| Software | Description |
|---|---|
| cwl-upgrader | Upgrade CWL documents from draft-3 to v1.0 |
| argparse2tool | Generate CWL CommandLineTool wrappers (and/or Galaxy tool descriptions) from Python programs that use argparse. Also supports the click argument parser. |
| cwl2argparse | Generate Python argparse code from CWL CommandLineTool description. |
| pypi2cwl | Automatically run argparse2cwl on any package in PyPi |
| acd2cwl | ACD (EMBOSS) to CWL generator |
| CTD converter | Common Tool Definition (CTD) to CWL converter |
| scriptcwl | Create CWL workflows by writing a simple Python script |
| cwl-to-parsl | Convert CWL to Parsl |
| Beatrice | Pipeline Assembler For CWL |
| zatsu-cwl-generator | A simple CWL document generator from given execution commands |
| Janis | A Python API that generates portable CWL and WDL workflows |
| cwl-utils | New Python 3.6+ CWL parsing library |
| ipython2cwl | a tool for converting IPython Jupyter Notebooks to CWL CommandLineTools via typing annotations |
| pegasus-cwl-converter | Work in progress tool to convert a CWL workflow into a Pegasus workflow. |
代码库
| Software | Description |
|---|---|
| cwltool | cwltool (can be imported as a Python module and extended to create custom cwl runners |
| schema salad | Python module and tools for working with the CWL schema. |
| cwljava | Java classes for loading, modifying, and creating CWL v1.2 documents |
| CWL for R | Parse and work with CWL from R |
| buchanae/cwl | CWL document parsing and processing utilities in Go. |
| CWL for Go | - |
| CWL for Scala | CWL object model for Scala |
| cwl-proto | Reading and writing Common Workflow Language to Protocol Buffers |
| CmdParser | Reading and Writing Common Workflow Language spec files from C++ applications. Includes a Command Line Parser |
| Rcwl | Build, read, write and run CWL in R |
| tidycwl | Tidy (R) Common Workflow Language Tools and Workflows |
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