snakemake-workflow-engine

Python-based workflow management system for reproducible, scalable pipelines. Define rules with file-based dependencies; Snakemake automatically determines the execution order and parallelism. Supports local, SLURM, LSF, AWS, and Google Cloud execution via profiles; per-rule conda/Singularity environments. Use for bioinformatics NGS pipelines, ML training workflows, and any multi-step file-processing analysis. Use Nextflow instead for Groovy-based dataflow pipelines or when nf-core ecosystem integration is required.