Ten simple rules and a template for creating workflows-as-applications

Abstract

As bioinformatics analyses increase in size and complexity, workflow managers are becoming more popular for building pipelines Workflow managers, such as Snakemake [4], Nextflow Workflow managers enable non-bioinformaticians to run published pipelines with confidence, and workflow managers with graphical user interfaces such as Galaxy [8] and BioWorkflow [9] have helped nonbioinformaticians create their own simple pipelines. Earlier tools for workflow management have been around for a while, including GNU Make, ruffus [10], doit However, the integration of cluster and cloud computing support in Snakemake, Nextflow, and Cromwell helped drive their current popularity. The use of workflow managers facilitates following the FAIR (Findable, Accessible, Interoperable, Reusable) guiding principles for open scientific research Interestingly, many existing bioinformatics command line tools are wrappers for a series of other software, but since that is the goal of workflow managers, they can be used instead. Examples of command line tools built on a workflow manager include Hecatomb These tools all consist of two key components: a convenience launcher, which provides the command line interface for the tool and compiles the configuration from user command line arguments, and the workflow pipeline and associated files, which performs the actual analysis.