BioShake: a Haskell EDSL forbioinformatics workflows

Justin Bedo

Abstract: Typical bioinformatics analyses comprise of long running computational workflows.An important part of reproducible research is the management and execution ofthese workflows to allow robust execution and to minimise errors. BioShake is anembedded domain specific language in Haskell for specifying and executing computa-tional workflows for bioinformatics that significantly reduces the possibility of errorsoccurring. Unlike other workflow frameworks, BioShake raises many properties tothe type level allowing the correctness of a workflow to be statically checked duringcompilation, catching errors before any lengthy execution process. BioShake buildson the Shake build tool to provide robust dependency tracking, parallel execution,reporting, and resumption capabilities. Finally, BioShake abstracts execution so thatjobs can either be executed directly or submitted to a cluster. BioShake is available athttp://github.com/PapenfussLab/bioshake.