BioShake: a Haskell EDSL for bioinformatics workflows

PeerJ

article

Justin Bedő¹ 

[1] Bioinformatics Division, The Walter and Eliza Hall Institute;Department of Computing and Information Systems, The University of Melbourne

关键词: Haskell;    Workflow;    EDSL;    Bioinformatics;    Reproducibility;   

DOI  :  10.7717/peerj.7223

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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. BioShake is available at http://github.com/PapenfussLab/bioshake.

【 授权许可】

CC BY