BioShake: a Haskell EDSL for bioinformatics workflows
BioShake: a Haskell EDSL for bioinformatics workflows
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DOI：
10.7717/peerj.7223
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发表时间：
2019-07-09
期刊：
影响因子：
2.7
通讯作者：
Bedo, Justin
中科院分区：
文献类型：
--
作者：
Bedo, Justin
典型的生物信息学分析包括长时间运行的计算工作流程。可重复研究的一个重要部分是管理和执行这些工作流程，以实现稳健的执行并最大限度地减少错误。 BioShake 是 Haskell 中的一种嵌入式领域特定语言，用于指定和执行生物信息学的计算工作流程，从而显着降低发生错误的可能性。 Unlike other workflow frameworks, BioShake raises many properties to the type level allowing the correctness of a workflow to be statically checked during compilation, catching errors before any lengthy execution process. BioShake 基于 Shake 构建工具构建，提供强大的依赖性跟踪、并行执行、报告和恢复功能。最后，BioShake 抽象执行，以便作业可以直接执行或提交到集群。
Typical bioinformatics analyses comprise of long running computational workflows. An important part of reproducible research is the management and execution of these workflows to allow robust execution and to minimise errors. BioShake is an embedded domain specific language in Haskell for specifying and executing computational workflows for bioinformatics that significantly reduces the possibility of errors occurring. Unlike other workflow frameworks, BioShake raises many properties to the type level allowing the correctness of a workflow to be statically checked during compilation, catching errors before any lengthy execution process. BioShake builds on the Shake build tool to provide robust dependency tracking, parallel execution, reporting, and resumption capabilities. Finally, BioShake abstracts execution so that jobs can either be executed directly or submitted to a cluster.