RESUMO
MOTIVATION: The volume of biomedical data generated each year is growing exponentially as high-throughput molecular, imaging and mHealth technologies expand. This rise in data volume has contributed to an increasing reliance on and demand for computational methods, and consequently to increased attention to software quality and data integrity. RESULTS: To simplify data verification in diverse data-processing pipelines, we created PipeVal, a light-weight, easy-to-use, extensible tool for file validation. It is open-source, easy to integrate with complex workflows, and modularized for extensibility for new file formats. PipeVal can be rapidly inserted into existing methods and pipelines to automatically validate and verify inputs and outputs. This can reduce wasted compute time attributed to file corruption or invalid file paths, and significantly improve the quality of data-intensive software. AVAILABILITY AND IMPLEMENTATION: PipeVal is an open-source Python package under the GPLv2 license and it is freely available at https://github.com/uclahs-cds/package-PipeVal. The docker image is available at: https://github.com/uclahs-cds/package-PipeVal/pkgs/container/pipeval.
Assuntos
Software , Fluxo de TrabalhoRESUMO
Summary: DNA sequencing is becoming more affordable and faster through advances in high-throughput technologies. This rise in data availability has contributed to the development of novel algorithms to elucidate previously obscure features and led to an increased reliance on complex workflows to integrate such tools into analyses pipelines. To facilitate the analysis of DNA sequencing data, we created metapipeline-DNA, a highly configurable and extensible pipeline. It encompasses a broad range of processing including raw sequencing read alignment and recalibration, variant calling, quality control and subclonal reconstruction. Metapipeline-DNA also contains configuration options to select and tune analyses while being robust to failures. This standardizes and simplifies the ability to analyze large DNA sequencing in both clinical and research settings. Availability: Metapipeline-DNA is an open-source Nextflow pipeline under the GPLv2 license and is freely available at https://github.com/uclahs-cds/metapipeline-DNA.