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Table 1 Advantages and disadvantages of different categories of automation strategies for bioinformatics

From: Experiences with workflows for automating data-intensive bioinformatics

 

Advantages

Disadvantages

Scripting

∙ Simple to construct

∙ Hard to hand over, manual tools integration and difficult HPC interaction

Makefile

∙ Simple to construct once you are familiar with the programming languages and the bioinformatics command-line tools involved

∙ Multithreaded programs and remote execution not handled well

 

∙ Describes data flow and takes care of dependency resolution, parallel execution and caching results from previous runs

∙ Lack of recursion support

 

∙ Uses code fragments in familiar scripting languages for processing of data

∙ Requires programming or shell experience

  

∙ Can’t be automatically parsed and visualized

Scientific Workflow Systems

∙ More powerful features, easier to maintain and share

∙ Requires more effort