Getting started with Snakemake
Exercise summary
Introduction - running a Snakemake workflow
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Objectives:
- learn how to run a small Snakemake pipeline
- understand the basic architecture of Snakemake files
- get familiar with the output & output log
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.
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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
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Objectives:
- fetching file names with glob_wildcards
- using a configuration file
- about directives and how to access their values
- capturing error and output streams (log)
- about re-running options
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Objectives:
- learn how to run Snakemake on multiple processors locally
- learn how to communicate with the Slurm 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
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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