Compendium Manager: a tool for coordination of workflow management instances for bulk data processing in Python
Richard J. Abdill, Ran Blekhman
Compendium Manager是一个用Python编写的命令行工具,用于自动配置,启动和评估生物信息学管道。 尽管Snakemake和Nextflow等工作流管理工具使用户能够在单个测序项目中自动处理样本,但批量集成许多数据集需要启动并监控数百或数千个管道。 我们介绍了 Compendium Manager,这是一种轻量级的命令行工具,可以大规模启动和监控分析管道。 该工具可以通过项目列表衡量进度,将结果加载到共享数据库中,并记录详细的处理指标,以便以后进行评估和可重复性。
Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and Nextflow enable users to automate the processing of samples within a single sequencing project, integrating many datasets in bulk requires launching and monitoring hundreds or thousands of pipelines. We present the Compendium Manager, a lightweight command-line tool to enable launching and monitoring...