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Janis: A Python framework for Portable Pipelines

Lupat, Richard; Franklin, Michael; Thomas, Evan; Kesumadewi, Juny; Yu, Jiaan; Bhuyan, Mohammad; Papenfuss, Tony; Park, Daniel; Pope, Bernard; Li, Jason

There are many frameworks for building bioinformatics pipelines, including the Common Workflow Language (CWL), Workflow Description Language (WDL), Nextflow and more. Each framework brings a community and a set of resources, including engines and other tools. The incompatibility of these frameworks poses considerable challenges for portability, where changing between systems requires substantial re-engineering efforts and is an inhibitor to sharing workflows. There are many external differences in these frameworks, such as implementation language, however they have a considerable overlap in their underlying features. 

Janis is an open-source Python framework that addresses this interoperability problem by abstracting the workflow model in order to generate CWL and WDL pipelines. The Janis API simplifies many aspects of building workflows and can mask idiosyncrasies of the target specifications while still allowing for rich workflow logic to be represented.

Janis includes two exemplar variant calling pipelines for calling germline and somatic variants.

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