Snakemake for Lattice Quantum Field Theory

Being able to reliably run a range of tools, across multiple inputs, and in the right order, is a very common problem in computing, including in scientific data analysis. If you develop scripts for data analysis from scratch, you will usually end up running up against these challenges. Rather than reinventing the wheel,we can lean on existing tools to do this for us, letting us focus on the aspects unique to our own work. Such tools are called workflow managers.

In this lesson, we introduce Snakemake, a workflow manager originally developed for bioinformatics applications, but that maps well onto the needs of data analysis in lattice quantum field theory.

By defining rules, each of which specify how to translate one or more input files into one or more output files, we can build up a workflow that takes our raw data as input, and produces plots, tables, and other definitions that we can include in our publications.

能够在多输入场景下按正确顺序可靠运行各类工具，是计算领域（涵盖科学数据分析）中极为普遍的问题。若从零编写数据分析脚本，通常都会遭遇此类挑战。与其重复造轮子，我们可依托现有工具完成相关工作，从而将精力聚焦于自身研究独有的环节。这类工具被称为工作流管理器（workflow manager）。

本课程将介绍Snakemake——一款最初为生物信息学应用开发的工作流管理器，但其同样能很好地适配格点量子场论（lattice quantum field theory）领域的数据分析需求。

通过定义规则（每条规则均指定如何将一个或多个输入文件转换为一个或多个输出文件），我们可构建一套以原始数据为输入，最终生成可用于学术发表的图表、表格及其他成果的工作流。