The seminar was organized by NGSchool and was livestreamed on Youtube. Follow along with the exercises in this github repository.
Snakemake is a Pythonic workflow engine developed by Johannes Köster. It has gained popularity for its concise syntax and robust execution.
Dr. David Koppstein 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.
To setup a minimal snakemake environment, first install Miniconda with Bioconda channels by following the instructions here.
Then, run
conda create -n ngstutorial -c bioconda snakemake
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.