Chapter 6

Reproducibility and Workflows

• Multi-omics integration

  Merging RNA-seq, proteomics, and methylation into one model only works if you pick the method for the question you're actually asking.

• Nextflow

  The workflow engine that turns "it ran on my laptop" into "it ran the same way on 10,000 samples across three clusters."

• Snakemake

  The workflow engine that turns a folder of one-off scripts into a DAG that only reruns what actually changed.