YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts

Authors:
  • TMTimothy McPhillips
    Timothy McPhillips
  • TSTianhong Song
    Tianhong Song
  • TKTyler Kolisnik
    Tyler Kolisnik
  • KBKhalid Belhajjame
    Khalid Belhajjame
  • RBR. Kyle Bocinsky
    R. Kyle Bocinsky
  • YCYang Cao
    Yang Cao
  • JCJames Cheney
    James Cheney
  • SDSaumen Dey
    Saumen Dey
  • JFJuliana Freire
    Juliana Freire
  • CJChristopher Jones
    Christopher Jones
Open Access
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Abstract
Scientific workflow management systems offer features for composing complex computational pipelines from modular building blocks, executing the resulting automated workflows, and recording the provenance of data products resulting from workflow runs. Despite the advantages such features provide, many automated workflows continue to be implemented and executed outside of scientific workflow systems due to the convenience and familiarity of scripting languages (such as Perl, Python, R, and MATLAB), and to the high productivity many scientists experience when using these languages. YesWorkflow is a set of software tools that aim to provide such users of scripting languages with many of the benefits of scientific workflow systems. YesWorkflow requires neither the use of a workflow engine nor the overhead of adapting code to run effectively in such a system. Instead, YesWorkflow enables scientists to annotate existing scripts with special comments that reveal the computational modules and dataflows otherwise implicit in these scripts. YesWorkflow tools extract and analyze these comments, represent the scripts in terms of entities based on the typical scientific workflow model, and provide graphical renderings of this workflow-like view of the scripts. Future version of YesWorkflow will also allow the prospective provenance of the data products of these scripts to be queried in ways similar to those available to users of scientific workflow systems.