April 2022
Beginner to intermediate
486 pages
10h 22m
Chinese
Content preview from 云端基因组学
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223
第
8
章
用工作流自动执行分析任务
本书至此，我们一直在终端手动运行单条命令。然而绝大多数基因组工作（更确切
地说是二次分析工作，从原始数据提炼信息，接着将其输入下游分析环节，以最终
生成生物学洞察力）都要按同一顺序在测序仪输出的所有数据上运行相同命令。回
顾第
6
、
7
章所讲
GATK
最佳实践工作流，试想对每个样本都要手动完成相关操作，
这差事该有多乏味。刚进入该领域的研究者，往往觉得在测试数据上逐步运行命令
对自己工作非常有帮助，因为他们可趁机领会关键步骤、要求和注意事项（这就是
我们为什么在第
6
、
7
章带你学习一遍命令），但最终你还是会希望能够自动完成其
中尽可能多的工作。自动化不仅减少你需手动完成的枯燥工作，还能增加你分析工
作的产出，并减少人工犯错机会。
本章将实现从单条命令或一次性脚本到可复用工作流的转变。我们将介绍工作流管
理系统
Cromwell
和工作流语言
WDL
的用法，我们选择这两者主要是考虑到它们好
移植。我们还将带你编写和执行你的第一个示例工作流，并解释
Cromwell
的输出。
接着，我们会编写并执行几个更真实工作流，运行
GATK
，使用分散—聚集并行机
制完成相同处理任务。
8.1 WDL
和
Cromwell
系统简介
你也许还记得我们在技术入门部分（第
3
章）介绍过工作流概念。正如当时所讲，
编写和运行工作流可用工具非常多，各有各的特性，优缺点也不尽相同。我们很难
224
｜
第
8
章
说哪个工具最好，因为工具的选择在很大程度上取决于特定背景和需求。本书选择
Cromwell
系统，搭配
WDL
使用，这对搭档最适合本书目标读者的广度和需求范围。 ...
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I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
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I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.