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
Workflow-as-output recognises that the orchestration of tools, data, and parameters is itself an intellectual contribution. Repositories such as WorkflowHub assign DOIs and enable citation. Increasingly accompanied by container images (Docker, Singularity) to ensure environment reproducibility.
References
- Goble et al. 2020 ‘FAIR Computational Workflows’ Data Intelligence
- WorkflowHub citation guidance
Also known as
Computational pipeline (output) · Analysis workflow
Machine-readable encodings
Use in your systems
xml
<role vocab="credit"
vocab-identifier="https://casrai.org/dictionary/"
vocab-term="Workflow (as output)"
vocab-term-identifier="https://casrai.org/dictionary/term/workflow-as-output" />json
{
"@context": "https://schema.org",
"@type": "DefinedTerm",
"name": "Workflow (as output)",
"identifier": "https://casrai.org/dictionary/term/workflow-as-output",
"description": "A computational workflow — a structured description of a multi-step analysis pipeline, expressed in a workflow language (Nextflow, Snakemake, CWL, WDL) or platform-specific format, with dependencies, parameters, and provenance — deposited in a repository with a persistent identifier as a citable research output.",
"inDefinedTermSet": "https://casrai.org/dictionary/domain/research-outputs-expanded/",
"url": "https://casrai.org/dictionary/term/workflow-as-output",
"sameAs": [
"Computational pipeline (output)",
"Analysis workflow"
],
"license": "https://creativecommons.org/licenses/by/4.0/"
}
