Nextflow is a workflow management system commonly used in fields like bioinformatics and earth observation. It coordinates distributed data processing of various tools as an acyclic sequence of tasks while using, containerization (e.g., Docker), orchestration (e.g., Kubernetes), or batch processing (e.g., SLURM). Monitoring such workflow executions can be challenging but aids performance analysis, debugging, and data provenance. Besides Nexflow's basic built-in monitoring, the wf-commons tool for creating wf-instances is widely regarded as the standard in the Nextflow community. The monitoring plugin we develpoed provides a more detailed and flexible alternative compatible with wf-instances while removing the need for a custom Nextflow fork by using Nextflow's plug-in mechanism (version 21.10), optional direct .jar file changes of static artifacts without recompilation and allows online monitoring during execution.
翻译:Nextflow是一种常用于生物信息学和地球观测等领域的流程管理系统。它协调各种工具的分布式数据处理,将其组织为无环任务序列,同时利用容器化(如Docker)、编排(如Kubernetes)或批处理(如SLURM)。监控此类工作流程执行具有挑战性,但有助于性能分析、调试和数据溯源。除Nextflow基本的内置监控外,用于创建wf-instances的wf-commons工具被广泛视为Nextflow社区的标准。我们开发的监控插件提供了与wf-instances兼容的更详细、更灵活的替代方案,同时通过使用Nextflow的插件机制(版本21.10)消除了对自定义Nextflow分支的需求,可选地直接修改静态工件的.jar文件而无需重新编译,并允许在执行期间进行在线监控。