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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