BIOI2-Training – Snakemake – Exercises – BIOI2 – Integrative BIOInformatics platforme

Getting started with Snakemake

About this course | Before the session | About Snakemake | Course material | Exercises

Exercise summary

Introduction - running a Snakemake workflow

Exercise 0: running an already-existing Snakemake pipeline

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Objectives:

learn how to fetch (setup) and run a small Snakemake pipeline (o1)
understand the basic architecture of Snakemake files (o2)
get familiar with the output log (o3)

Introduction - building your own Snakemake workflow file

This exercise is divided into 3 parts. In part 1, you will learn how to create a first basic pipeline. In the following parts, you will build on this same pipeline and improve it.

Exercise 1A: create a Snakefile from scratch

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Objectives:

learn about rules and basic workflow concepts
learn how rules are linked thanks to input/output files, and the use of a target rule
learn how to generalise the inputs of a rule, and the expand function
learn how to visualise your pipeline
learn how to simulate the execution with dry-run

Exercise 1B: improving your first Snakefile

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Objectives:

fetching file names with glob_wildcards (o1)
using a configuration file (o2)
about directives and how to access their values (o2)
capturing error and output streams (log) (o3)
about re-running options (o4)

Exercise 1C: scaling up your workflow to an HPC environment

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Objectives:

learn how to run Snakemake on multiple processors locally
learn how to communicate with the OpenPBS scheduler on the I2BC cluster
learn how to control the software environment
create a profile for Snakemake
learn how to set resources specific for each rule

Bonus: From bash script to snakemake

Exercise 2: create a basic workflow for RNA-seq analysis

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Objectives:

reinforce Snakemake concepts learnt in the previous exercises
learn how to adapt already existing shell scripts into a Snakemake workflow

Don’t hesitate to look through Snakemake’s documentation for any concepts your are not sure about. There’s also a page dedicated to the recommended practices with file organisation etc. in Snakemake here and here.