The invention relates to bioinformatics pipelines and wrapper scripts that call executables in those pipelines and that also identify beneficial changes to the pipelines. A tool in a pipeline has a smart wrapper that can cause the tool to analyze the sequence data it receives but that can also select a change to the pipeline when circumstances warrant. In certain aspects, the invention provides a system for genomic analysis. The system includes a processor coupled to a non-transitory memory. The system is operable to present to a user a plurality of genomic tools organized into a pipeline. At least a first one of the tools comprises an executable and a wrapper script. The system can receive instructions from the user and sequence data—instructions that call for the sequence data to be analyzed by the pipeline—and select, using the wrapper script, a change to the pipeline.