Bioinformatics workflow for the detection of eQTL in the cattle genome using Nextflow DSL2

The in silico detection of expression quantitative trait loci (eQTL) demands high throughput processing from hundreds of samples, which is often a challenge to handle and run such large datasets. In order to focus on the core analysis, it is convenient to have simple coding and hassle-free installation of different software tools required for the bioinformatics workflow. In this context, the newly available technologies like workflow managers and software containers enabled to develop workflows with less complexity. In this study, we developed an eQTL bioinformatics pipeline with the workflow manager Nextflow and docker container software, for coding and installing the required software tools. This workflow can be portable to a different computer environment, and the results are reproducible. We tested the functionality of our workflow with a sample dataset and the runtime estimates from this demo run will provide important information in planning future analyses with much larger datasets.