工具插件

Vim WDL 插件

broadinstitute官方提供了在Vim环境下的WDL插件，提供基础的关键词、语法高亮等功能。其安装方式，可参考 https://github.com/broadinstitute/vim-wdl

VScode WDL 插件

VScode也提供了WDL语言的插件。用户可直接通过VScode插件管理进行安装。

WDL 语法校验工具

WOMtool 可以对WDL脚本进行语法校验，其网站为 https://cromwell.readthedocs.io/en/stable/WOMtool/

1 2	# 通过conda安装 conda install -c "bioconda/label/cf201901" womtool

CWL 转化 WDL

目前，除了WDL之外，也有相当一部分生物信息流程是以CWL语言编写的。用户可以采用dxCompiler将CWL脚本转化为WDL脚本。https://github.com/dnanexus/dxCompiler

调度引擎

cromwell

1 2	# 通过conda安装 conda install -c "bioconda/label/cf201901" cromwell

widdler

widdler GitHub
Widdler is a command-line tool for executing WDL workflows on Cromwell servers.
Features include:

Workflow execution: Execute a workflow on a specified Cromwell server.
Workflow restart: Restart a previously executed workflow.
Workflow queries: Get the status, metadata, or logs for a specific workflow.
Workflow result explanation: Get more detailed information on fails at the command line.
Workflow monitoring: Monitor a specific workflow or set of user-specific workflows to completion.
Workflow abortion: Abort a running workflow.
JSON validation: Validate a JSON input file against the WDL file intended for use.

一个demo示例

helloword.wdl

helloword.wdl

task echo {
  String out
  command {
    echo Hello World! > ${out}
  }
  output {
    File outFile = "${out}"
  }
}
workflow wf_echo {
  call echo
  output {
    echo.outFile
  }
}

执行操作

# 生成配置文件（json格式）
womtool inputs  helloword.wdl > helloword.wdl.input.json
# 编辑配置文件
vi helloword.wdl.input.json
# {
#  "wf_echo.echo.out": "Demo-Test"
# }
# 运行任务
cromwell run  helloword.wdl -i helloword.wdl.input.json