ngsschool-snakemake-tutorial

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ngsschool-snakemake-tutorial

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Snakemake Tutorial for NGSSchool.

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# NGSchool Seminar

The seminar was organized by [NGSchool](https://ngschool.eu/ngseminars/) and was livestreamed on [Youtube](https://www.youtube.com/watch?v=h2CJ-qr8fjs). Follow along with the exercises in this github repository.

# About Snakemake

[Snakemake](https://snakemake.readthedocs.io/en/stable/) is a Pythonic workflow engine developed by Johannes Köster. It has gained popularity for its concise syntax and robust execution.

# About the Presenter

[Dr. David Koppstein](www.davidkoppstein.com) is a researcher at the Berlin Institute of Medical Systems Biology and a graduate of MIT. Although originally trained as a wet lab biologist, he is also enthusiastic about Python and reproducible research.

# Setup

To setup a minimal snakemake environment, first install Miniconda with Bioconda channels by following the instructions [here](https://bioconda.github.io/user/install.html).

Then, run

```
conda create -n ngstutorial -c bioconda snakemake
```

# Exercises

Minimal examples corresponding to the slides can be found in the exercises folder. To run them, use:

```
conda activate ngstutorial
snakemake --printshellcmds -- all
```

For dummy rules, run them using the `-n` flag.

For rules with wrappers, use `--use-conda`.

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