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

• DOI: 10.1371/journal.pcbi.1010705
• Publication Date: 2022-12-15T18:30:41Z
• Authors: Michael J. Roach; N. Tessa Pierce-Ward; Radoslaw Suchecki; Vijini Mallawaara...; Bhavya Papudeshi; Scott A. Handley; C. Titus Brown; Nathan S. Watson-...; Robert A. Edwards
• Keywords: Graphical user interface

As bioinformatics analyses increase in size and complexity, workflow managers are becoming more popular for building pipelines [1][2][3].Workflow managers, such as Snakemake [4], Nextflow [5], Cromwell [6] with WDL or CWL [7], empower researchers to build robust that call a series of tools scripts perform bespoke analysis.Workflow enable non-bioinformaticians run published confidence, graphical user interfaces Galaxy [8] BioWorkflow [9] have helped nonbioinformaticians create their own simple pipelines.Earlier management been around while, including GNU Make, ruffus [10], doit [11], rake ruby [12], Makeflow [13].However, the integration cluster cloud computing support Snakemake, Nextflow, drive current popularity.The use facilitates following FAIR (Findable, Accessible, Interoperable, Reusable) guiding principles open scientific research [14].Interestingly, many existing command line wrappers other software, but since is goal they can be used instead.Examples built on manager include Hecatomb [15,16], ATLAS [17], VirSorter2 [18], spacegraphcats [19], BlobToolKit [20], PGAP [21].These all consist two key components: convenience launcher, which provides interface tool compiles configuration from arguments, pipeline associated files, performs actual analysis.Developing software much quicker easier when not reinventing wheel.For instance, if needs parse GenBank file, it better code process manually, simply load library designed robustly validate these files?The same concept applies how runs.It possible write functions compare file timestamps add reentrancy catch error codes, throw meaningful messages system calls fail, cleanup intermediate allow interaction job scheduling system, steps isolated containers, etc.When were still infancy, authors several genome