Bioinformatics Workflows For Life Sciences Using Snakemake

Everything else will be explained in the course.

Description
Course on snakemake. snakemake is a modern workflow language that is widely used in acad and industrial circles to build reproducible, legible, portable, interoperable and efficient pipelines in bioinformatics and beyond. The course closely follows the basic bioinformatics workflow described in the official snakemake tutorial but takes a step-by-step approach and delves deeply into each feature of the snakemake language. It covers:- installation- Snakefile- rules- directives: input, output, shell, script- target files- creation of a directed acyclic graphThis course does not cover:- benchmarking- conda directive- snakemake profiles for cluster computers- temporary files- parameters- resourcesAt the end of this course, you will be able to build a basic bioinformatics pipeline. This knowledge will be sufficient to make a positive difference in your day-to-day life as a bioinformatician. It will also prepare you for my advanced course on snakemake.The course is primarily intended for bioinformaticians but it can also be useful for people from other fields who want to build pipelines.The course can also be used as an introduction to the field of bioinformatics. In it, I use the concepts of "reads", "alignment", "BAM" files, "VCF" files, variant calls. However, note that I do not spend much explaining those concepts and focus primarily on the snakemake language.

Overview
Section 1: Introduction

Lecture 1 Introduction

Section 2: Setup

Lecture 2 Installing conda

Lecture 3 Preparing a working directory

Lecture 4 Creating an environment with the required software

Section 3: Basics: an example workflow

Lecture 5 Step 1: Mapping reads without snakemake

Lecture 6 Step 1: my first snakemake rule

Lecture 7 Step 1: snakemake automatically creates the necessary parent directories

Lecture 8 Step 1: rule and directive definitions are indented

Lecture 9 Step 1: when is a target file generated

Lecture 10 Step 1: brace notation in the shell directive

Lecture 11 Step 2: generalising a snakemake rule to make it work with infinitely many files

Lecture 12 Step 2: list target files in snakemake command

Lecture 13 Step 2: situations in which the snakemake workflow in run

Lecture 14 Step 3: add second snakemake rule

Lecture 15 Step 3: split shell directive command over several lines

Lecture 16 Step 4: add third rule

Lecture 17 Step 4: visualise DAG

Lecture 18 Step 5: named input files

Lecture 19 Step 5: naming input files becomes necessary when there are many of them

Lecture 20 Step 5: aggregate input files with the expand helper function

Lecture 21 Step 5: aggregate input files over all combinations of variables with expand

Lecture 22 Step 5: aggregate input files over "zip" combinations of variables with expand

Lecture 23 Step 6: using custom scripts

Lecture 24 Step 7: adding a target rule

Section 4: Launch a snakemake workflow

Lecture 25 Options to use when launching a snakemake workflow

Section 5: Possible snakemake errors and how to resolve them

Lecture 26 R_LIBS environment variable is set

Lecture 27 bash strict mode

Lecture 28 no config file given

Section 6: Visualise the snakemake workflow

Lecture 29 Rule graph

Bioinformaticians who want to learn how to create clean, efficient and reproducible pipelines.

HomePage:

https://www.udemy.com/course/snakemake/

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