Python-based workflow manager for reproducible, scalable pipelines. Define rules with file-based dependencies; Snakemake resolves execution order and parallelism. Runs local, SLURM, LSF, AWS, GCP via profiles; per-rule conda/Singularity envs. For NGS pipelines, ML training, and multi-step file processing. Use Nextflow for Groovy dataflow or nf-core integration.
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Snakemake — Python Workflow Engine
Overview
Snakemake is a Python-based workflow management system that scales analyses from laptop to HPC and cloud. Workflows are defined as rules with explicit input/output file dependencies; Snakemake resolves the execution order automatically and runs independent steps in parallel. Rules can call shell commands, Python/R/Julia scripts, or inline Python. Per-rule conda or Singularity environments make workflows fully reproducible. Widely used in bioinfo
[Description truncada. Veja o README completo no GitHub.]