Investigating reproducibility and tracking provenance – A genomic workflow case study

BMC Bioinformatics

Research Article

Richard O. Sinnott¹  Sehrish Kanwal¹  Farah Zaib Khan¹  Andrew Lonie² 

[1] Department of Computing and Information Systems, The University of Melbourne, 3010, Melbourne, VIC, Australia;Melbourne Bioinformatics, The University of Melbourne, 3010, Melbourne, VIC, Australia;

关键词: Reproducibility;    Provenance;    Workflow;    Galaxy;    Cpipe;    Common Workflow Language (CWL);   

DOI  :  10.1186/s12859-017-1747-0

 received in 2017-03-23, accepted in 2017-07-04,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundComputational bioinformatics workflows are extensively used to analyse genomics data, with different approaches available to support implementation and execution of these workflows. Reproducibility is one of the core principles for any scientific workflow and remains a challenge, which is not fully addressed. This is due to incomplete understanding of reproducibility requirements and assumptions of workflow definition approaches. Provenance information should be tracked and used to capture all these requirements supporting reusability of existing workflows.ResultsWe have implemented a complex but widely deployed bioinformatics workflow using three representative approaches to workflow definition and execution. Through implementation, we identified assumptions implicit in these approaches that ultimately produce insufficient documentation of workflow requirements resulting in failed execution of the workflow. This study proposes a set of recommendations that aims to mitigate these assumptions and guides the scientific community to accomplish reproducible science, hence addressing reproducibility crisis.ConclusionsReproducing, adapting or even repeating a bioinformatics workflow in any environment requires substantial technical knowledge of the workflow execution environment, resolving analysis assumptions and rigorous compliance with reproducibility requirements. Towards these goals, we propose conclusive recommendations that along with an explicit declaration of workflow specification would result in enhanced reproducibility of computational genomic analyses.

【 授权许可】

CC BY   
© The Author(s). 2017