Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline DOI Creative Commons
Yash Patel, Chenghao Zhu, Takafumi N. Yamaguchi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 7, 2024

DNA sequencing continues to get cheaper and faster. In parallel, algorithmic innovations have allowed inference of a wide range nuclear, mitochondrial, somatic evolutionary from data. To make automated, high-quality more readily available, we created an extensible Nextflow meta-pipeline called metapipeline-DNA. Metapipeline-DNA supports processing raw reads through alignment, variant detection, quality control subclonal reconstruction. Each step quality-control, data-visualization multiple algorithms. is cloud-compatible highly configurable, with options subsect, optimize analyses, including automated failure-recovery. enables high-scale, fault-tolerant, comprehensive analysis genome sequencing. Availability: open-source pipeline under the GPLv2 license available at https://github.com/uclahs-cds/metapipeline-DNA.

Language: Английский

NFTest: automated testing of Nextflow pipelines DOI Creative Commons
Yash Patel, Chenghao Zhu, Takafumi N. Yamaguchi

et al.

Bioinformatics, Journal Year: 2024, Volume and Issue: 40(2)

Published: Feb. 1, 2024

Abstract Motivation The ongoing expansion in the volume of biomedical data has contributed to a growing complexity tools and technologies used research with an increased reliance on complex workflows written orchestration languages such as Nextflow integrate algorithms into processing pipelines. use involving various led scrutiny software development practices avoid errors individual connections between them. Results To facilitate test-driven pipelines, we created NFTest, framework for automated pipeline testing validation customizability options features. It is open-source, easy initialize use, customizable allow test success configurable through broad range assertions. NFTest simplifies burden developers by automating tests once defined providing flexible interface running validate workflows. This reduces barrier rigorous workflow paves way toward reducing computational biomedicine. Availability implementation open-source Python under GPLv2 license freely available at https://github.com/uclahs-cds/tool-NFTest. call-sSNV at: https://github.com/uclahs-cds/pipeline-call-sSNV.

Language: Английский

Citations

8
Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline DOI Creative Commons
Yash Patel, Chenghao Zhu, Takafumi N. Yamaguchi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 7, 2024

DNA sequencing continues to get cheaper and faster. In parallel, algorithmic innovations have allowed inference of a wide range nuclear, mitochondrial, somatic evolutionary from data. To make automated, high-quality more readily available, we created an extensible Nextflow meta-pipeline called metapipeline-DNA. Metapipeline-DNA supports processing raw reads through alignment, variant detection, quality control subclonal reconstruction. Each step quality-control, data-visualization multiple algorithms. is cloud-compatible highly configurable, with options subsect, optimize analyses, including automated failure-recovery. enables high-scale, fault-tolerant, comprehensive analysis genome sequencing. Availability: open-source pipeline under the GPLv2 license available at https://github.com/uclahs-cds/metapipeline-DNA.

Language: Английский

Citations

2