Pipelines on The Augmented Scholar

Snakemake — Reproducible Pipelines in Python

Fri, 17 Jul 2026 00:00:00 +0000

Overview

Snakemake is Make reborn for science with Python syntax: you declare rules (inputs → outputs → command), and it builds the dependency graph, runs only outdated steps, and parallelises automatically. The same Snakefile runs on your laptop and submits to SLURM.

Nextflow — Pipelines Built for Scale

Fri, 17 Jul 2026 00:00:00 +0000

Overview

Nextflow expresses pipelines as dataflow between processes, each optionally running in its own container, with executors for SLURM, Kubernetes, and every major cloud. Its ace is nf-core: community-curated production pipelines (RNA-seq, variant calling, and 100+ more) you can run rather than rewrite.