STAPLER: a simple tool for creating, managing and parallelizing common high-throughput sequencing workflows

Abstract

STAPLER is a command line program intended for creating, managing and parallelizing bioinformatics workflows. Considerable emphasis has been placed on the ease of adoption and use by effortless installation, simple definition of workflows and quick-start tutorials. Custom workflows can be defined in an easy, modular way allowing the user to choose the desired input data, analysis tools and parameters with a simple parameter file. STAPLER then generates shell scripts that execute the workflow on a personal computer or in a supercomputing environment. Log files are generated to ensure that experimental results can be reproduced, and features are provided for validating run success and allowing rerunning parts of workflow if necessary. STAPLER is freely available on the web at https://github.com/tyrmi/STAPLER, implemented in Python 2 and supported on any UNIX or UNIX-like platform.