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 |