【9.3.1】cwl 概况

两个主要的教程,还没完全整理

一. 简介

Common Workflow Language简称CWL

官网:https://www.commonwl.org

github:https://github.com/common-workflow-language/common-workflow-language

二. 安装

方式1

gitclone https://github.com/common-workflow-language/cwltool.git # clone cwltool repo

cd cwltool# Switch to source directory

pip install .# Install `cwltool` from source

cwltool--version# Check if the installation works correctly

方式2

pip install cwltool

三 使用方法

user guide:https://www.commonwl.org/user_guide/

cwltool [tool-or-workflow-description] [input-job-settings]

cwl文件需要写成json或yaml格式,或者两者的混合。YAML文件编写格式参考YAML Guide。

需要两个cwl文件,一个进行流程说明,一个设置输入输出和参数。

示例:

hello_world.cwl

cwlVersion: v1.2

# What type of CWL process we have in this document.
class: CommandLineTool
# This CommandLineTool executes the linux "echo" command-line tool.
baseCommand: echo

# The inputs for this process.
inputs:
  message:
    type: string
    # A default value that can be overridden, e.g. --message "Hola mundo"
    default: "Hello World"
    # Bind this message value as an argument to "echo".
    inputBinding:
      position: 1
outputs: []

运行:

$ cwltool hello_world.cwl

INFO /opt/hostedtoolcache/Python/3.9.14/x64/bin/cwltool 3.1.20221008225030
INFO Resolved 'hello_world.cwl' to 'file:///home/runner/work/user_guide/user_guide/src/_includes/cwl/hello_world.cwl'
INFO [job hello_world.cwl] /tmp/_aziq13k$ echo \
    'Hello World'
Hello World
INFO [job hello_world.cwl] completed success
{}
INFO Final process status is success

传参方式1:

$ cwltool hello_world.cwl --message="Hola mundo"

INFO /opt/hostedtoolcache/Python/3.9.14/x64/bin/cwltool 3.1.20221008225030
INFO Resolved 'hello_world.cwl' to 'file:///home/runner/work/user_guide/user_guide/src/_includes/cwl/hello_world.cwl'
INFO [job hello_world.cwl] /tmp/uwridbjx$ echo \
    'Hola mundo'
Hola mundo
INFO [job hello_world.cwl] completed success
{}
INFO Final process status is success

传参方式2:

hello_world-job.json

{
  "message": "test"
}

运行命令:

$ cwltool hello_world.cwl hello_world-job.json

INFO /opt/hostedtoolcache/Python/3.9.14/x64/bin/cwltool 3.1.20221008225030
INFO Resolved 'hello_world.cwl' to 'file:///home/runner/work/user_guide/user_guide/src/_includes/cwl/hello_world.cwl'
INFO [job hello_world.cwl] /tmp/vmuqlnt8$ echo \
INFO [job hello_world.cwl] completed success
{}
INFO Final process status is success

3.1 YAML Guide

(1)Key-Value Pairs

冒号分割,比如first_key: value1, value2

key不能有空格,value可以有

需注意数字,如果是integer可以写123,如果要strings要写"123"。在CWL中所有的baseCommand都需要是strings,所以必须加引号:baseCommand: [echo, “42”]

(2)Commemts

用#可注释掉右侧内容

(3)Maps

在编写流程时,会建立一个复杂的map,用YAML格式进行分级,下一级“children”属于上一级“parent”,用两个空格进行缩进,不能用tab。

(4)Arrays

用-来为一个key提供多个value或objects(key-value对)。

参考资料

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