接下來多個(gè)章節(jié)都是基于 v1.1語法

主要的介紹方法有點(diǎn)類似借鑒Python Cookbook，采取提出問題-解決問題，從實(shí)戰(zhàn)中學(xué)會WDL

• 問題1: 通過egrep抓取文件中含有特定pattern的行
• 解決代碼：
  • 運(yùn)行的腳本：egrep.wdl

version 1.0
task hello {
    # 定義輸入
    input {
        String pattern
        File in
    }
    # 相關(guān)命令
    command <<<
        # 當(dāng)執(zhí)行有問題立刻終止
        set -e
        egrep '~{pattern}' '~{in}'
    >>>
    # 相關(guān)輸出
    output {
        Array[String] matches = read_lines(stdout())
    }
}

workflow wf {
    input {
        File infile
        String pattern
    }
    call hello {
        input: 
            in=infile,
            pattern=pattern
    }
    output {
        Array[String] matches = hello.matches
    }
}

• 輸入json

{
    "wf.pattern": "^[a-z]+$",
    "wf.infile": "/Users/your_name/cromwell/00.question1/file.txt"
}

• 執(zhí)行及輸出信息

$ java -jar cromwell-57.jar run egrep.wdl --inputs egrep.json
...
[2021-03-29 17:59:48,60] [info] SingleWorkflowRunnerActor workflow finished with status 'Succeeded'.
{
  "outputs": {
    "wf.matches": ["abcdef", "fhhh", "hhh"]
  },
  "id": "c8898489-99f0-41f2-bec4-7a3d0a36c6dc"
}
...

• 問題2: 通過egrep抓取文件中含有特定pattern的行，并行處理文件
  主要是修改wf地方：

workflow wf_parallel {
    input {
        Array[File] files
        String pattern
    }
    scatter (path in files){
        call hello {
            input: 
                in=path,
                pattern=pattern
        }       
    }
    output {
        Array[Array[String]] all_matches = hello.matches
    }
}

多個(gè)文件輸入的json文件如下(一定要用絕對路徑)

{
    "wf_parallel.pattern": "^[a-z]+$",
    "wf_parallel.infile": ["/Users/liji/cromwell/00.question1/file.txt", "/Users/liji/cromwell/00.question1/file2.txt"]
}

• 執(zhí)行及輸出信息

$ java -jar /Users/liji/cromwell/cromwell-57.jar run egrep2.wdl --inputs egrep2.json
...
{
  "wf_parallel.all_matches": [["abcdef", "fhhh", "hhh"], ["abcdefaaaaa", "fhhheeee", "hhhgggg"]]
}
...