在
workflow myWorkflow {
call myTask
}
task myTask {
command {
echo "hello world"
}
output {
String out = read_string(stdout())
}
} 对于一个
每个脚本包含1个
在 1. task 中的参数下面的示意图中,task 有3个输入的参数,文件类型的 2. workflow 中的参数下面的示意图中, 作为流程管理语言,需要对多个 1. 一对一的依赖关系前一个
workflow LinearChain {
File firstInput
call stepA { input: in=firstInput }
call stepB { input: in=stepA.out }
call stepC { input: in=stepB.out }
}
task stepA {
File in
command { programA I=${in} O=outputA.ext }
output { File out = "outputA.ext" }
}
task stepB {
File in
command { programB I=${in} O=outputB.ext }
output { File out = "outputB.ext" }
}
task stepC {
File in
command { programC I=${in} O=outputC.ext }
output { File out = "outputC.ext" }
} 一个
workflow MultiOutMultiIn {
File firstInput
call stepA { input: in=firstInput }
call stepB { input: in=stepA.out }
call stepC { input: in1=stepB.out1, in2=stepB.out2 }
}
task stepA {
File in
command { programA I=${in} O=outputA.ext }
output { File out = "outputA.ext" }
}
task stepB {
File in
command { programB I=${in} O1=outputB1.ext O2=outputB2.ext }
output {
File out1 = "outputB1.ext"
File out2 = "outputB2.ext" }
}
task stepC {
File in1
File in2
command { programB I1=${in1} I2=${in2} O=outputC.ext }
output { File out = "outputC.ext" }
} 2. 多对多的依赖关系一个 示例如下: workflow BranchAndMerge {
File firstInput
call stepA { input: in=firstInput }
call stepB { input: in=stepA.out }
call stepC { input: in=stepA.out }
call stepD { input: in1=stepC.out, in2=stepB.out }
}
task stepA {
File in
command { programA I=${in} O=outputA.ext }
output { File out = "outputA.ext" }
}
task stepB {
File in
command { programB I=${in} O=outputB.ext }
output { File out = "outputB.ext" }
}
task stepC {
File in
command { programC I=${in} O=outputC.ext }
output { File out = "outputC.ext" }
}
task stepD {
File in1
File in2
command { programD I1=${in1} I2=${in2} O=outputD.ext }
output { File out = "outputD.ext" }
} 3. 平行关系多个 示例如下: workflow ScatterGather {
Array[File] inputFiles
scatter (oneFile in inputFiles) {
call stepA { input: in=oneFile }
}
call stepB { input: files=stepA.out }
}
task stepA {
File in
command { programA I=${in} O=outputA.ext }
output { File out = "outputA.ext" }
}
task stepB {
Array[File] files
command { programB I=${files} O=outputB.ext }
output { File out = "outputB.ext" }
}
workflow taskAlias {
File firstInput
File secondInput
call stepA as firstSample { input: in=firstInput }
call stepA as secondSample { input: in=secondInput }
call stepB { input: in=firstSample.out }
call stepC { input: in=secondSample.out }
}
task stepA {
File in
command { programA I=${in} O=outputA.ext }
output { File out = "outputA.ext" }
}
task stepB {
File in
command { programB I=${in} O=outputB.ext }
output { File out = "outputB.ext" }
}
task stepC {
File in
command { programC I=${in} O=outputC.ext }
output { File out = "outputC.ext" }
} 在WDL脚本中, 理论上每个 掌握以上几点,就可以理解一个
最新版的下载链接如下:
第一步是得到输入参数的列表,用法如下
用
总结
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