snakemake_examples/README.md @ master
| 428015d2 | Chloe Quignot | # Examples and solutions of the Snakemake BIOI2 training session
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Instructions are on the BIOI2 website: https://bioi2.i2bc.paris-saclay.fr/training/snakemake/
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To download this repository, open a terminal and type:
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```bash
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git clone https://forge.i2bc.paris-saclay.fr/git/bioi2_formations/snakemake_examples.git
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```
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## Organisation of this repository
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```text
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├── README.md
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├── exercise0
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├── exercise0_improved_after_1A
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├── exercise0_improved_after_1B
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├── exercise0_improved_after_1C
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└── demo_advanced
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```
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### Exercise 0
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The example Snakemake pipeline to execute in [Exercise 0](https://bioi2.i2bc.paris-saclay.fr/training/snakemake/exercises/exercise-0-objective) is in the `exercise0` folder.
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**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.
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### Exercise 2
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The `demo_advanced` folder is an example solution for Exercise 2 comprising several different types of syntaxes that you could encounter in Snakefiles.
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## Executing the SnakeFiles
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If you're in the folder that contains the Snakefile (and if the Snakefile is named Snakefile), you can just type:
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```bash
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snakemake --cores 1
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```
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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):
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```bash
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snakemake --cores 1 -s /path/to/snakefile.smk
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```
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