agile parallel bioinformatics workflow management using pwrake敏捷并行使用pwrake生物信息学工作流管理.pdfVIP

Mishima et al. BMC Research Notes 2011, 4:331 /1756-0500/4/331 TECHNICAL NOTE Open Access Agile parallel bioinformatics workflow management using Pwrake Hiroyuki Mishima1,2*, Kensaku Sasaki1,2, Masahiro Tanaka3,4, Osamu Tatebe3,4,5 and Koh-ichiro Yoshiura1 Abstract Background: In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby’s standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings: We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the d