This repository contains the snakemake workflow used to perform the genome-wide association study described in the publication. Once the pipeline has been successfully executed, the figures can be recreated using the Jupyter notebook supplied.
Diricks, M., Petersen, S., Bartels, L. et al. Revisiting mutational resistance to ampicillin and cefotaxime in Haemophilus influenzae. Genome Med 16, 140 (2024). https://doi.org/10.1186/s13073-024-01406-4
Please install miniconda first. Afterwards run
conda create -n hinf --file environment.yml
to install all the packages required to run the pipeline.
The pipeline was implemented using the workflow manager snakemake.
Run the following command to execute the pipeline:
snakemake --cores <number of cores> --use-conda
After the execution is finished, all results can be found in the subfolder named results.