Fig. 2

SPEAQeasy workflow diagram. A simplified workflow diagram for each pipeline execution. The red box indicates the FASTQ files are inputs to the pipeline; green coloring denotes major output files from the pipeline; the remaining boxes represent computational steps. Yellow-colored steps are optional or not always performed; for example, preparing a particular set of annotation files occurs once and uses a cache for further runs. Finally, blue-colored steps are ordinary processes which occur on every pipeline execution. The workflow proceeds downward, and each row in the diagram implicitly represents the ability for several computation steps to execute in parallel