We ensured that no bioinformatics knowledge is needed to understand the tutorial.Īlso have a look at the corresponding slides. However, Snakemake is a general-purpose workflow management system for any discipline. The examples presented in this tutorial come from Bioinformatics.
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Hence, a Snakemake workflow scales without modification from single core workstations and multi-core servers to cluster or batch systems.įinally, Snakemake integrates with the package manager Conda and the container engine Singularity such that defining the software stack becomes part of the workflow itself. The syntactic extensions provided by Snakemake maintain this property for the definition of the workflow.įurther, Snakemake’s scheduling algorithm can be constrained by priorities, provided cores and customizable resources and it provides a generic support for distributed computing (e.g., cluster or batch systems). The Python language is known to be concise yet readable and can appear almost like pseudo-code. This allows to combine the flexibility of a plain scripting language with a pythonic workflow definition. Hooking into the Python interpreter, Snakemake offers a definition language that is an extension of Python with syntax to define rules and workflow specific properties. Snakemake sets itself apart from other text-based workflow systems in the following way.
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Snakemake follows the GNU Make paradigm: workflows are defined in terms of rules that define how to create output files from input files.ĭependencies between the rules are determined automatically, creating a DAG (directed acyclic graph) of jobs that can be automatically parallelized. Korean forms are used for the number of items from 1 to 60 and age.This tutorial introduces the text-based workflow system Snakemake. So books, people, trees, and any number of objects also use the Korean numbers. However, most objects are counted using the Korean system unless the counting involves money.So, for example, the word 10 might be spoken using two entirely different words depending on what’s being counted.
![counter in step 7 v5.6 counter in step 7 v5.6](https://upload.wikimedia.org/wikipedia/commons/c/cf/Complete_blood_count_and_differential.jpg)
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X Research source Thus, the Roman alphabet spellings of the words vary from site-to-site and are phonetic. Korean numbers are written using symbols that are called “Hangul” and are not written using the Roman alphabet.X Research source In most cases, if you are simply counting from 1 to 10 (and are not using money or other special cases), you will want to use the Korean system (this is also true in Taekwondo). In Korean, you will encounter two completely different sets of words for numbers, one based on Korean words and one related to Chinese (this system is sometimes called Sino-Korean).