PT  - JOURNAL ARTICLE
AU  - Justin Bedő
TI  - Bioshake: a Haskell EDSL for bioinformatics pipelines
AID  - 10.1101/529479
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 529479
4099  - http://biorxiv.org/content/early/2019/01/24/529479.short
4100  - http://biorxiv.org/content/early/2019/01/24/529479.full
AB  - Background Typical bioinformatics analysis comprise long running computational pipelines. An important part of producing reproducible research is the management and execution of these computational pipelines to allow robust execution and to minimise errors. Bioshake is an embedded domain specific language embedded in Haskell for specifying and executing computational pipelines in bioinformatics that significantly reduces the possibility of errors occurring.Results Unlike other pipeline frameworks, Bioshake raises many properties to the type level to allow the correctness of a pipeline to be statically checked during compilation, catching errors before any lengthy execution process. Bioshake builds on the Shake build tool to provide robust dependency tracking, parallel execution, reporting, and resumption capabilities. Finally, Bioshake abstracts execution so that jobs can either be executed directly or submitted to a cluster.Conclusions Bioshake is available at http://github.com/papenfusslab/bioshake.BAMBinary Alignment MapCWLCommon Workflow LanguageDRMAADistributed Resource Management Application API [Troger et al., 2007]EDSLEmbedded Domain Specific LanguageSAMSequence Alignment Map