eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts

Chitneedi, Praveen Krishna; Hadlich, Frieder; Moreira, Gabriel C. M.; Espinosa-Carrasco, José; Li, Changxi; Plastow, Graham; Fischer, Daniel; Charlier, Carole; Rocha, Dominique; Chamberlain, Amanda J.; Kuehn, Christa

doi:http://dx.doi.org/10.1093/nargab/lqae122

eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts

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Citation

Chitneedi PK, Hadlich F, Moreira GCM, Espinosa-Carrasco J, Li C, Plastow G, et al. eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts. NAR Genom Bioinform. 2024 Sep 24;6(3):lqae122. DOI: 10.1093/nargab/lqae122

Abstract

Bioinformatic pipelines are becoming increasingly complex with the ever-accumulating amount of Next-generation sequencing (NGS) data. Their orchestration is difficult with a simple Bash script, but bioinformatics workflow managers such as Nextflow provide a framework to overcome respective problems. This study used Nextflow to develop a bioinformatic pipeline for detecting expression quantitative trait loci (eQTL) using a DSL2 Nextflow modular syntax, to enable sharing the huge demand for computing power as well as data access limitation across different partners often associated with eQTL studies. Based on the results from a test run with pilot data by measuring the required runtime and computational resources, the new pipeline should be suitable for eQTL studies in large scale analyses.