CWL User Guide 5: Capturing Standard Output

Common Workflow Language User Guide: Capturing Standard Output

今回は標準出力を、ファイルに書き込む例が書かれています

この回にでてくる主なキーワード

stdout
type: stdout

CWLファイル、

stdout.cwl

# !/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
baseCommand: echo
stdout: output.txt
inputs:
  message:
    type: string
    inputBinding:
      position: 1
outputs:
  output:
    type: stdout

パラメータファイル

echo-job.yml

message: Hello world!

実行

実行方法

cwltool stdout.cwl echo-job.yml

実行結果

$ cwltool stdout.cwl echo-job.yml
/usr/local/bin/cwltool 1.0.20171107133715
Resolved 'stdout.cwl' to 'file:///home/vagrant/cwl_user_guide_work/05-stdout/stdout.cwl'
[job stdout.cwl] /tmp/tmpP1A7UY$ echo \
    'Hello world!' > /tmp/tmpP1A7UY/output.txt
[job stdout.cwl] completed success
{
    "output": {
        "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
        "basename": "output.txt",
        "location": "file:///home/vagrant/cwl_user_guide_work/05-stdout/output.txt",
        "path": "/home/vagrant/cwl_user_guide_work/05-stdout/output.txt",
        "class": "File",
        "size": 13
    }
}
Final process status is success

実行結果確認

$ cat output.txt
Hello world!

今回使ったファイル

cwl_user_guide_work/05-stdout at master · manabuishii/cwl_user_guide_work