ArticleBioinformatics (Oxford, England)2024
NFTest: automated testing of Nextflow pipelines.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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.
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Who cites it
11 citing papers in PubMed.
- Comprehensive analysis of the gastric metatranscriptome reveals specific viral signatures associated with gastric cancer.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Article
- Identification of non-canonical peptides with moPepGen.Nature biotechnology · 2026Article
- Metapipeline-DNA: A comprehensive germline and somatic genomics Nextflow pipeline.Cell reports methods · 2026Article
- 96 sample parallel acoustic fragmentation for high throughput next generation sequencing library preparation.PloS one · 2026Article
- Integrating Artificial Intelligence in Next-Generation Sequencing: Advances, Challenges, and Future Directions.Current issues in molecular biology · 2025Review
- Identification of non-canonical peptides with moPepGen.bioRxiv : the preprint server for biology · 2025Article
- Improving the reliability, quality, and maintainability of bioinformatics pipelines with nf-test.GigaScience · 2025Article
- StableLift: Optimized Germline and Somatic Variant Detection Across Genome Builds.bioRxiv : the preprint server for biology · 2024Article
- The landscape of drug sensitivity and resistance in sarcoma.Cell stem cell · 2024Article
- PipeVal: light-weight extensible tool for file validation.Bioinformatics (Oxford, England) · 2024Article
- Multi-Omics Unveils the Dual-Life of the Aquatic Plant Potamogeton nodosus.Physiologia plantarumArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
motivationThe ongoing expansion in the volume of biomedical data has contributed to a growing complexity in the tools and technologies used in research with an increased reliance on complex workflows written in orchestration languages such as Nextflow to integrate algorithms into processing pipelines. The growing use of workflows involving various tools and algorithms has led to increased scrutiny of software development practices to avoid errors in individual tools and in the connections between them.
resultsTo facilitate test-driven development of Nextflow pipelines, we created NFTest, a framework for automated pipeline testing and validation with customizability options for Nextflow features. It is open-source, easy to initialize and use, and customizable to allow for testing of complex workflows with test success configurable through a broad range of assertions. NFTest simplifies the testing burden on developers by automating tests once defined and providing a flexible interface for running tests to validate workflows. This reduces the barrier to rigorous biomedical workflow testing and paves the way toward reducing computational errors in biomedicine. AVAILABILITY AND IMPLEMENTATION: NFTest is an open-source Python framework under the GPLv2 license and is freely available at https://github.com/uclahs-cds/tool-NFTest. The call-sSNV Nextflow pipeline is available at: https://github.com/uclahs-cds/pipeline-call-sSNV.
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What OpenQuestion holds
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.