WDL - 撰写语法

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和其他编程语法一样，WDL也存在不同版本间的语法差异，因此在使用WDL进行流程撰写时，需要明确参考的版本规范
所以后文语法如无特殊标准，本文想过内容均基于 WDL v1.0 版本。

变量类型

基础变量(primitive types )

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Int i = 0                  # An integer value
Float f = 27.3             # A floating point number
Boolean b = true           # A boolean true/false
String s = "hello, world"  # A string value
File f = "path/to/file"    # A file

复合变量(compound types)

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# In the examples below P represents any of the primitive types above, and X and Y represent any valid type (even nested compound types)
Array[X] xs = [x1, x2, x3]                    # An array of Xs
Map[P,Y] p_to_y = { p1: y1, p2: y2, p3: y3 }  # A map from Ps to Ys
Pair[X,Y] x_and_y = (x, y)                    # A pair of one X and one Y
Object o = { "field1": f1, "field2": f2 }     # Object keys are always `String`s

自定义结构（Struct Definition）

struct是一种类似c的构造，它允许用户创建由先前存在的类型组成的新的复合类型。然后，可以在Task或Workflow定义中使用struct作为声明来代替任何其他常规类型。在许多情况下，结构体替代了Object类型，并允许对其成员进行适当的类型设置。

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struct SampleData{}

复合类型还可以在结构中使用，以便轻松地将它们封装在单个对象中。

Json Type 2 WDL Type

JSON Type WDL Type
object Map[String, ?]
array Array[?]
number Int or Float
string String
boolean Boolean
null ???

object转换成Map存疑，测试过程中，使用object的方式可以正常，但是使用map的遍历方式失败。

示例Demo存档

可以看到WDL本身提供了比较充足的变量类型，但是由于wdl本身对于文本/变量的处理函数非常匮乏，因此无法像snakemake一样，在读取数据后进行自定义的数据处理构造需要的数据结构。因此针对wdl应用到生信检测过程时，一些复杂的逻辑关系需要提前梳理形成特定的数据结构，本文记录一些学习开发阶段，接触的复杂数据结构和 WDL 解析方式，以备后用。

样本文库下机数据多层依赖关系

最终生效的输入文件格式（json），通过wdl解析成object + 数组，实现多层结构实现。

单样本解析

输入的文本文件.json

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{
        "cancer":[{
                "LibID":"1C-Lib-1",
                "LibData":[["FastqA1","FastqA2"],["FastqB1","FastqB2"],["FastqC1","FastqC2"],["FastqD1","FastqD2"]]
                },{
                "LibID":"1C-Lib-2",
                "LibData":[["L2FastqA1","L2FastqA2"],["L2FastqB1","L2FastqB2"],["L2FastqC1","L2FastqC2"]]
                }],
        "normal":[{
                "LibID":"1N-Lib-1",
                "LibData":[["NFastqA1","NFastqA2"],["NFastqB1","NFastqB2"],["NFastqC1","NFastqC2"]]
                }]
}

解析脚本.wdl

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version 1.0

workflow wf_echo {
        input{
                File data
        }

        Object All_Sample = read_json(data)

        scatter ( singleLin in All_Sample.cancer){
                String lib = singleLin.LibID
                Array[Array[String]] FastqList = singleLin.LibData

                scatter (singleFastq in FastqList){
                        Array[String] Fastq = singleFastq
                        call echoa as cancer_fastq{
                                input:
                                        Fastq=Fastq
                        }

                }
                call Singlelib as Cancer_lib{
                        input:
                                lib = lib,
                                Fastq = cancer_fastq.outputa

                }
        }

        call Singlelib as Cancer_sample{
                input:
                        lib = "All_cancer",
                        Fastq = Cancer_lib.Tag
        }
}

task Singlelib {
        input{
                String lib
                Array[String]  Fastq
        }
        String out = lib + ".txt"
        String sample = lib
        command <<<
                echo  ~{sep="," Fastq} > ~{sample}.txt
        >>>

        output {
                String outFile = out
                String Tag  = lib
        }
}

task echoa {
        input{
                Array[String] Fastq
        }
                String Fastq1=Fastq[0]
                String Fastq2=Fastq[1]
        command <<<
                echo ~{Fastq1}  ~{Fastq2}
        >>>
        output{
                String outputa=Fastq1+":"+Fastq2
        }
}

执行示例脚本

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[2023-02-09 20:13:43,87] [info] BackgroundConfigAsyncJobExecutionActor [70365163wf_echo.cancer_fastq:0:1]: echo L2FastqA1  L2FastqA2
[2023-02-09 20:13:43,87] [info] BackgroundConfigAsyncJobExecutionActor [3956881dwf_echo.cancer_fastq:3:1]: echo FastqD1  FastqD2
[2023-02-09 20:13:43,87] [info] BackgroundConfigAsyncJobExecutionActor [70365163wf_echo.cancer_fastq:2:1]: echo L2FastqC1  L2FastqC2
[2023-02-09 20:13:43,87] [info] BackgroundConfigAsyncJobExecutionActor [3956881dwf_echo.cancer_fastq:2:1]: echo FastqC1  FastqC2
[2023-02-09 20:13:43,87] [info] BackgroundConfigAsyncJobExecutionActor [3956881dwf_echo.cancer_fastq:0:1]: echo FastqA1  FastqA2
[2023-02-09 20:13:43,87] [info] BackgroundConfigAsyncJobExecutionActor [70365163wf_echo.cancer_fastq:1:1]: echo L2FastqB1  L2FastqB2
[2023-02-09 20:13:43,87] [info] BackgroundConfigAsyncJobExecutionActor [3956881dwf_echo.cancer_fastq:1:1]: echo FastqB1  FastqB2

[2023-02-09 20:13:50,36] [info] 70365163-898e-417f-b7a7-7ce6866b4dae-SubWorkflowActor-SubWorkflow-ScatterAt45_12:1:1 [70365163]: Workflow ScatterAt45_12 complete. Final Outputs:
{
  "cancer_fastq.outputa": ["L2FastqA1:L2FastqA2", "L2FastqB1:L2FastqB2", "L2FastqC1:L2FastqC2"],
  "Fastq": [["L2FastqA1", "L2FastqA2"], ["L2FastqB1", "L2FastqB2"], ["L2FastqC1", "L2FastqC2"]]
}
[2023-02-09 20:13:50,36] [info] 3956881d-5958-469c-bd04-e4f41509fd51-SubWorkflowActor-SubWorkflow-ScatterAt45_12:0:1 [3956881d]: Workflow ScatterAt45_12 complete. Final Outputs:
{
  "Fastq": [["FastqA1", "FastqA2"], ["FastqB1", "FastqB2"], ["FastqC1", "FastqC2"], ["FastqD1", "FastqD2"]],
  "cancer_fastq.outputa": ["FastqA1:FastqA2", "FastqB1:FastqB2", "FastqC1:FastqC2", "FastqD1:FastqD2"]
}


[2023-02-09 20:14:03,75] [info] BackgroundConfigAsyncJobExecutionActor [00e87cbbwf_echo.Cancer_lib:1:1]: echo  L2FastqA1:L2FastqA2,L2FastqB1:L2FastqB2,L2FastqC1:L2FastqC2 > 1C-Lib-2.txt
[2023-02-09 20:14:03,75] [info] BackgroundConfigAsyncJobExecutionActor [00e87cbbwf_echo.Cancer_lib:0:1]: echo  FastqA1:FastqA2,FastqB1:FastqB2,FastqC1:FastqC2,FastqD1:FastqD2 > 1C-Lib-1.txt

[2023-02-09 20:14:13,74] [info] BackgroundConfigAsyncJobExecutionActor [00e87cbbwf_echo.Cancer_sample:NA:1]: echo  1C-Lib-1,1C-Lib-2 > All_cancer.txt

[2023-02-09 20:14:18,89] [info] WorkflowExecutionActor-00e87cbb-2f53-4a0e-ae74-4ff2d8eaf88c [00e87cbb]: Workflow wf_echo complete. Final Outputs:
{
  "wf_echo.cancer_fastq.outputa": [["FastqA1:FastqA2", "FastqB1:FastqB2", "FastqC1:FastqC2", "FastqD1:FastqD2"], ["L2FastqA1:L2FastqA2", "L2FastqB1:L2FastqB2", "L2FastqC1:L2FastqC2"]],
  "wf_echo.lib": ["1C-Lib-1", "1C-Lib-2"],
  "wf_echo.Cancer_sample.Tag": "All_cancer",
  "wf_echo.Fastq": [[["FastqA1", "FastqA2"], ["FastqB1", "FastqB2"], ["FastqC1", "FastqC2"], ["FastqD1", "FastqD2"]], [["L2FastqA1", "L2FastqA2"], ["L2FastqB1", "L2FastqB2"], ["L2FastqC1", "L2FastqC2"]]],
  "wf_echo.Cancer_lib.Tag": ["1C-Lib-1", "1C-Lib-2"],
  "wf_echo.Cancer_lib.outFile": ["1C-Lib-1.txt", "1C-Lib-2.txt"],
  "wf_echo.Cancer_sample.outFile": "All_cancer.txt",
  "wf_echo.FastqList": [[["FastqA1", "FastqA2"], ["FastqB1", "FastqB2"], ["FastqC1", "FastqC2"], ["FastqD1", "FastqD2"]], [["L2FastqA1", "L2FastqA2"], ["L2FastqB1", "L2FastqB2"], ["L2FastqC1", "L2FastqC2"]]]
}

批次多样本解析

wdl在解析json时，最外层总会强制解析成一个object（输入 list 也无法识别为Array进行scatter操作），所以顶层必须使用object。

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{"All_Sample":[{
        "sampleID":"SampleA",
        "cancer":[{
                "LibID":"1C-Lib-1",
                "LibData":[["FastqA1","FastqA2"],["FastqB1","FastqB2"],["FastqC1","FastqC2"],["FastqD1","FastqD2"]]
                },{
                "LibID":"1C-Lib-2",
                "LibData":[["L2FastqA1","L2FastqA2"],["L2FastqB1","L2FastqB2"],["L2FastqC1","L2FastqC2"]]
                }],
        "normal":[{
                "LibID":"1N-Lib-1",
                "LibData":[["NFastqA1","NFastqA2"],["NFastqB1","NFastqB2"],["NFastqC1","NFastqC2"]]
                }]
},{
        "sampleID":"SampleB",
        "cancer":[{
                "LibID":"1C-Lib-1",
                "LibData":[["FastqA1","FastqA2"],["FastqB1","FastqB2"],["FastqC1","FastqC2"],["FastqD1","FastqD2"]]
                },{
                "LibID":"1C-Lib-2",
                "LibData":[["L2FastqA1","L2FastqA2"],["L2FastqB1","L2FastqB2"],["L2FastqC1","L2FastqC2"]]
                }],
        "normal":[{
                "LibID":"1N-Lib-1",
                "LibData":[["NFastqA1","NFastqA2"],["NFastqB1","NFastqB2"],["NFastqC1","NFastqC2"]]
                }]
}]
}

解析脚本

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version 1.0

workflow wf_echo {
        input{
                File data
        }
        Object All_Sample = read_json(data)
        scatter (singlesample in All_Sample.All_Sample){
                String sampleID = singlesample.sampleID
                scatter (singleLin in singlesample.cancer){
                        String Type = "cancer"
                        String lib = singleLin.LibID
                        Array[Array[String]] FastqList = singleLin.LibData

                        scatter (singleFastq in FastqList){
                                Array[String] Fastq = singleFastq
                                call echoa as cancer_fastq{
                                        input:
                                                Fastq=Fastq
                                }

                        }
                        call Singlelib as Cancer_lib{
                                input:
                                        sample = sampleID,
                                        Type = Type,
                                        lib = lib,
                                        Fastq = cancer_fastq.outputa

                        }
                }

                call Singlelib as Cancer_sample{
                        input:
                                sample = sampleID,
                                Type = "cancer",
                                lib = "All_lib",
                                Fastq = Cancer_lib.Tag
                }

        }
        call Singlelib as sample_level{
                input:
                        sample = "All_sample",
                        Type = "All_type",
                        lib = "All_case",
                        Fastq = Cancer_sample.Tag
        }
}

task Singlelib {
        input{
                String sample
                String Type
                String lib
                Array[String]  Fastq
        }
        String out = lib + ".txt"
        command <<<
                echo  ~{sep="," Fastq} > ~{sample}.txt
        >>>

        output {
                String outFile = out
                String Tag  = lib
        }
}

task echoa {
        input{
                Array[String] Fastq
        }
                String Fastq1=Fastq[0]
                String Fastq2=Fastq[1]
        command <<<
                echo ~{Fastq1}  ~{Fastq2}
        >>>
        output{
                String outputa=Fastq1+":"+Fastq2
        }
}

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