Polyploidy, the presence of multiple genome copies as a result of whole-genome-duplications, is often thought to cause immediate repruductive isolation between polyploids and diploid relatives, due to inviability and sterility of hybrid offspring. However, recent research showed evidence of introgression (gene-flow via hybridization and backcrossing) between diploid and polyploid lineages. In this seminar I will introduce my PostDoc project, which uses population genomic analyses to quantify the degree of introgression between multiple natural plant lineages with variable ploidy and assess to what degree it can contribute to adaptive evolution. In order to determine the degree of inter-ploidy introgression, variant calling and subsequent population genomic analyses have to be run for each non-model species in a ploidy-aware manner. These analyses require complex custom bioinformatics pipelines, which have to be run repeatedly for multiple lineages on HPC computing clusters. Implementing and running these types of workflows in an efficient and reproducible manner can be challenging. As an approach to overcome these issues I will introduce Snakemake, which allows to implement automated, scalable and reproducible bioinformatics workflows.