Running snakemake-simple-mapping on CERN REANA – FORGE technical deployment and compatibility guide

Technical guide documenting how the MPUSP snakemake-simple-mapping workflow (v1.8.0), a reference genomics pipeline for read alignment, quality control, variant calling and annotation, was executed on the CERN REANA reproducible analysis platform within the FORGE project. The native REANA Snakemake engine could not parse the workflow, so the adopted solution runs a REANA Serial step inside a versioned container maintained by Area Science Park (ghcr.io/ritareasciencepark/forge-snakemake:0.1), where a modern Snakemake installation executes the workflow and creates rule-specific Conda environments. The guide covers: environment setup and vendoring of the workflow; compatibility patches; the driver container image; the reana.yaml configurations (dry run and full run); resource tuning; a troubleshooting table and reproducibility notes. It is intended for researchers and infrastructure operators who want to run Snakemake workflows on REANA or adapt the same approach to other workflows and computing environments. FORGE (Distributed data management for Genomics in the EOSC Federation) was funded within the Cascading Grants of the EOSC Gravity Project (Horizon Europe, Grant Agreement No. 101188045).