ArticleGigaScience2025
Improving the reliability, quality, and maintainability of bioinformatics pipelines with nf-test.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
1 citing paper in PubMed.
- Umi-pipeline-nf: a modular and scalable workflow for UMI-tagged nanopore amplicon analysis with real-time sequencing integration and GPU-acceleration.Bioinformatics (Oxford, England) · 2026Article
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Authors and funding
2 authors.
Funding
Abstract
backgroundThe workflow management system Nextflow, together with the nf-core community, has established an essential ecosystem in bioinformatics. However, ensuring the correctness and reliability of large and complex Nextflow pipelines remains challenging due to the lack of a unified, automated unit-testing framework.
resultsTo address this gap, we present nf-test, a modular testing framework for bioinformatics workflows. It enables users to test process blocks, workflow patterns, and entire pipelines in isolation while validating their outputs. Built with a syntax similar to Nextflow DSL2, nf-test offers unique features such as snapshot testing and smart testing, which optimize resource usage by testing only modified modules. We demonstrate across multiple pipelines that these features minimize development time, reduce test execution time by up to 80%, and enhance software quality by identifying bugs and issues early in the development process.
conclusionsAlready adopted by numerous pipelines, nf-test significantly improves the robustness, maintainability, and reliability of bioinformatics pipelines.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.