Onboarding snakemake: Progress towards WfExS-backend integration

Workflow Execution Service Backend (WfExS-backend) is a high-level workflow orchestrator designed for reproducible and secure workflow executions in isolated environments, promoting analysis reproducibility and replicability using potentially sensitive data. Through a user-friendly command line interface, WfExS fetches and materialises all necessary elements for workflow instantiation, including publicly available workflows, workflow engines, software containers, and reachable inputs, identified via URLs or stable permanent identifiers (CURIEs). Currently, WfExS exclusively supports both Nextflow and cwltool engines, so it is restricted to workflows written in Nextflow or CWL. There is an ongoing effort to integrate snakemake engine, in order to support snakemake workflows. However, integrating a new workflow engine poses multifaceted challenges. Ensuring compatibility with existing infrastructure, encompassing language syntax, containerization strategies, and execution models, is paramount.  Furthermore, Snakemake workflows introspection, incorporating their modular structure, available wrappers and subworkflows, presents a significant hurdle, while preserving overall workflow coherence. Validating consistency and reproducibility adds another layer of complexity to the integration process, requiring meticulous testing and verification procedures to ensure consistent and reliable workflow outcomes across multiple executions. Nevertheless, comprehensive documentation and community support streamline the integration process. Successfully incorporating Snakemake into WfExS-backend expands the software versatility and utility for scientific communities relying on this workflow engine, thereby advancing its mission of promoting analysis reproducibility and replicability across different workflows engines and scientific ecosystems in secure environments.