Although sequencing technology has become widely available in recent years, the steps in bioinformatics pipelines are time-consuming and barely standardized. New tools to improve individual steps in a pipeline are frequently published and configurations can be quickly adapted to use new versions. We performed case studies with a representative set of pipeline management tools using the GEP-R pipeline, and a qualitative study of different software packages covering relevant classes of software tools. We use a software toolset of R environment, Docker, KNIME, and BPEL to review our first aim of technical and organizational challenges. We propose snapshotting, documentation management, and a hybrid approach for our second aim of approaches to reproducibility. In order to have fully reproducible results derived from raw data, we think that it is necessary to archive biomedical analysis pipelines and their necessary software components.
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