Implementing nf-core pipelines within the Windows Subsystem for Linux (WSL) environment involves configuring a Linux distribution (typically Ubuntu) within Windows to execute nextflow pipelines. This setup allows users to leverage the reproducibility and scalability offered by nf-core without requiring a dedicated Linux machine. It entails installing WSL, choosing a Linux distribution, installing necessary dependencies like Nextflow, Conda or Mamba, and ensuring proper configuration of file system access between Windows and the Linux subsystem.
Utilizing this approach provides a streamlined and cost-effective solution for researchers and bioinformaticians using Windows operating systems. It eliminates the need for dual-boot systems or virtual machines, simplifying the workflow and minimizing resource overhead. Historically, bioinformatics pipelines were primarily developed and executed in Linux environments; this approach bridges the gap, making nf-core pipelines accessible to a broader user base and facilitating collaboration across diverse computational environments.
