CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language

Abstract: Massive growth in the amount of research data and computational analysis has led to increased utilization of pipeline managers in biomedical computational research. However, each of more than 100 such managers uses its own way to describe pipelines, leading to difficulty porting workflows to different environments and therefore poor reproducibility of computational studies. For this reason, the Common Workflow Language (CWL) was recently introduced as a specification for platform-independent workflow description, and work began to transition existing pipelines and workflow managers to CWL. Here, we present CWL-Airflow, an extension for the Apache Airflow pipeline manager supporting CWL. CWL-Airflow utilizes CWL v1.0 specification and can be used to run workflows on standalone MacOS/Linux servers, on clusters, or on variety cloud platforms. A sample CWL pipeline for processing of ChIP-Seq data is provided. CWL-Airflow is available under Apache license v.2 and can be downloaded from https://github.com/Barski-lab/cwl-airflow.