nextflow

Nextflow

Overview

Nextflow is a workflow language and runtime for building reproducible, portable, scalable data pipelines. It is dominant in bioinformatics but works for any data-heavy computation. nf-core is a community curating production-grade Nextflow pipelines, reusable modules, and the nf-core tooling on top of Nextflow.

Key ideas:

• Dataflow programming: pipelines are process tasks connected by channels. Nextflow infers execution order and parallelism from data dependencies — there is no explicit scheduler to write.
• Write once, run anywhere: the same pipeline runs locally, on HPC (SLURM, SGE, LSF, PBS), and on cloud (AWS Batch, Google Batch, Azure Batch, Kubernetes) by changing config/profiles, not code.
• Reproducibility: pinned software environments and pipeline revisions, immutable inputs/references, recorded parameters and seeds. -resume is a computational cache, not scientific validation. Conda is an environment manager; Wave resolves/builds images rather than executing them.
• DSL2 is the modern, required syntax: modular process/workflow/include definitions.

This skill covers both running existing pipelines and developing your own (Nextflow language + nf-core conventions, testing with nf-test, configuration, and deployment).

When to Use This Skill