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Published November 1, 2021 | Version v1
Working paper Open

10 Simple Rules for making a software tool workflow-ready

  • 1. Department of Computer Science, The University of Manchester, Manchester, UK
  • 2. Melandra Limited, UK
  • 3. Department of Computer Science, The University of Manchester, Manchester, UK; University of Amsterdam, Amsterdam, The Netherlands
  • 4. Research IT, The University of Manchester, Manchester, UK
  • 5. Meise Botanic Garden, Meise, Belgium
  • 6. Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
  • 7. Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Frei-burg, Germany
  • 8. Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden


Workflows have become a core part of computational scientific analysis in recent years. Automated computational workflows multiply the power of researchers, potentially turning “hand-cranked” data processing by informaticians into robust factories for complex research output.

However, in order for a piece of software to be usable as a workflow-ready tool, it may require alteration from its likely origin as a standalone tool. Research software is often created in response to the need to answer a research question with the minimum expenditure of time and money in resource-constrained projects. The level of quality might range from “it works on my computer” to mature and robust projects with support across multiple operating systems.

Despite significant increase in uptake of workflow tools, there is little specific guidance for writing software intended to slot in as a tool within a workflow; or on converting an existing standalone research-quality software tool into a reusable, composable, well-behaved citizen within a larger workflow.

In this paper we present 10 simple rules for how a software tool can be prepared for workflow use.


Accepted at PLOS Computational Biology (PCOMPBIOL-D-21-01704)



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BioExcel-2 – BioExcel Centre of Excellence for ComputationalBiomolecular Research 823830
European Commission
EOSC-Life – Providing an open collaborative space for digital biology in Europe 824087
European Commission
SYNTHESYS PLUS – Synthesis of systematic resources 823827
European Commission