Examples
Worked examples
- Is an instance
A Nextflow pipeline for bulk RNA-seq deposited to WorkflowHub with a DOI and DOI-cited in a paper
Counter-examples
Looks similar, but isn't
- Not an instance
A bash script with no documentation or repository is not a workflow-as-output in the citable sense
Editorial commentary
A workflow-as-output is a computational workflow — a structured, multi-step analysis pipeline expressed in a workflow language (Nextflow, Snakemake, the Common Workflow Language, or WDL) or a platform-specific format, with its dependencies, parameters, and provenance recorded — deposited in a repository with a persistent identifier and treated as a citable research output. The underlying recognition, set out in Goble et al.’s 2020 “FAIR Computational Workflows,” is that the orchestration of tools, data, and parameters into a reproducible pipeline is itself an intellectual contribution distinct from either the raw data or the resulting figures.
A research office is most likely to see a workflow output cited from a repository such as WorkflowHub, which assigns DOIs specifically for this purpose and provides citation guidance modelled on dataset citation practice. Workflows are increasingly accompanied by a matching container image, since the workflow definition alone does not guarantee the exact software environment it was run in will still be reproducible years later.
How it relates to sibling output types
- vs. Container image (as output) — the workflow is the sequence of analytical steps; the container image is the environment those steps ran in. Depositing both together closes most of the reproducibility gap either leaves open alone.
- vs. Dataset (as output) / Model (as output) — a workflow is typically what produced or analysed a dataset or model, not the dataset or model itself.
References
- Goble et al., “FAIR Computational Workflows,” Data Intelligence (2020).
- WorkflowHub citation guidance.
Also known as
Computational pipeline (output) · Analysis workflow
Machine-readable encodings
Use in your systems
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