Examples
Worked examples
- Is an instance
An nf-core/rnaseq pipeline run on AWS Batch using Singularity images.
- Is an instance
A custom Nextflow workflow distributed alongside a paper with a pinned configuration profile.
Counter-examples
Looks similar, but isn't
- Not an instance
A Snakemake pipeline (different ecosystem).
- Not an instance
A non-workflow shell script.
Editorial commentary
Nextflow is a workflow orchestration system built around dataflow programming: a pipeline is expressed as a set of processes connected by channels, and each process runs automatically as soon as its required input data become available, rather than following a fixed, manually-ordered execution sequence. It uses a Groovy-based domain-specific language and was originally developed at the Centre for Genomic Regulation (CRG) in Barcelona; it is now maintained and commercially supported by Seqera Labs, and underpins the nf-core project, a large, community-curated collection of standardised, peer-reviewed genomics analysis pipelines.
How this differs from a container image
Nextflow is a workflow language and execution engine — it decides what runs, in what order, and where (a local machine, an HPC cluster, or a cloud batch service). A container image is a separate mechanism, typically invoked by a Nextflow pipeline to pin each individual process’s software environment; a Nextflow pipeline definition commonly specifies which container image each process should run inside, combining the two mechanisms rather than substituting one for the other. Nextflow is also distinct from the portable, engine-agnostic interchange formats CWL and WDL: those are declarative specifications intended to run on multiple different engines, while Nextflow is a language tightly coupled to its own execution engine.
Why it matters for research administration
A published Nextflow pipeline, pinned to specific container images and a specific nf-core release, is a concrete, checkable reproducibility artefact — reviewers and funders can verify that the exact analysis pipeline is available, not merely described in prose.
References
- Di Tommaso, P. et al. (2017). “Nextflow enables reproducible computational workflows.” Nature Biotechnology 35, 316-319.
- See also: Snakemake (concept), Workflow language (CWL/WDL), Container image (Docker/Singularity/Apptainer).
Also known as
Nextflow
Machine-readable encodings
Use in your systems
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