Examples and solutions of the Snakemake BIOI2 training session

Instructions are on the BIOI2 website: https://bioi2.i2bc.paris-saclay.fr/training/snakemake/

To download this repository, open a terminal and type:

git clone https://forge.i2bc.paris-saclay.fr/git/bioi2_formations/snakemake_examples.git

Organisation of this repository

├── README.md
├── exercise0
├── exercise0_improved_after_1A
├── exercise0_improved_after_1B
├── exercise0_improved_after_1C
└── demo_advanced

Exercise 0

The example Snakemake pipeline to execute in Exercise 0 is in the exercise0 folder.

exercise0_improved_after_1X folders are examples of improvements of the initial SnakeFile after applying what you've learnt in Exercises 1A, 1B and 1C. We advise you to have a look at them once you've finished with the forementioned exercises.

Exercise 2

The demo_advanced folder is an example solution for Exercise 2 comprising several different types of syntaxes that you could encounter in Snakefiles.

Executing the SnakeFiles

If you're in the folder that contains the Snakefile (and if the Snakefile is named Snakefile), you can just type:

snakemake --cores 1

If you'd like to specify the Snakefile in the command line (because it's not in your current directory or because it's named differently):

snakemake --cores 1 -s /path/to/snakefile.smk