Question

我想用cwl（通用工作流语言）编写一个简单的命令包装器。我想做以下例子：

wc input.txt > input.txt.wc
wc some_folder/some_other_input > some_folder/some_other_input.wc

所以，基本上我希望代码在输入文件名后添加.wc并将其用作输出文件名。我写了下面的代码，但它没有用。（见下面的错误信息）。任何人都知道如何解决它？

wc2.cwl

cwlVersion: cwl:draft-3
class: CommandLineTool
baseCommand: wc
inputs:
  - id: inputfile
    type: File
    inputBinding:
      position: 1
  - id: outfilename
    type: string
      inputBinding:
        valueFrom: ${ $(inputs.inputfile.path) + '.wc' }
outputs:
  - id: outputfile
    type: File
    outputBinding:
      glob: $(inputs.outfilename)
stdout: $(inputs.outfilename)

WC2-job1.yml

inputfile:
  class: File
  path: input.txt

生成

$ cwl-runner wc2.cwl wc2-job1.yml
/home/ec2-user/venv/cwl/bin/cwl-runner 1.0.20160504183010
I'm sorry, I couldn't load this CWL file, try again with --debug for more information.
mapping values are not allowed here
  in "file:///home/ec2-user/cwl.examples/hello.workflow2/wc2.cwl", line 11, column 19

Answer 1

stdout：$（inputs.outfilename）成为， stdout：$（inputs ['outfilename']）

Answer 2

根据Common Workflow Language User Guide: Capturing Standard Output 和https://www.commonwl.org/v1.0/CommandLineTool.html#stdout中列出的示例，要指定用于捕获标准输出的文件名，请定义stdout: filename和outputs: type: stdout：

wc2.cwl

cwlVersion: cwl:v1.0
class: CommandLineTool
baseCommand: wc
inputs:
  - id: inputfile
    type: File
    inputBinding:
      position: 1
outputs:
  - id: outputfile
    type: stdout
stdout: $(inputs.inputfile.basename).wc

通过使用cwl修改输入字符串来指定stdout

2 个答案: