uap -- Universal Analysis Pipeline

Authors

Christoph Kämpf, Michael Specht, Alexander Scholz, Sven-Holger Puppel, Gero Doose, Kristin Reiche, Jana Schor, Jörg Hackermüller

uap: reproducible and robust HTS data analysis. BMC Bioinformatics 20, 664 (2019)

Introduction

The uap package is a framework to configure, run, and control large data multi-step analyses. Its main focus is on the analysis of high-throughput sequencing data.

The aim of this data processing pipeline is to enable robust and straightforward bioinformatics data evaluation. It is implemented in Python, runs under GNU/Linux and can be controlled from the command-line interface. Although the primary focus is the evaluation of sequencing data, its design allows for a variety of other applications.

About this Repository

This repository contains the development status of uap at Fraunhofer IZI. It is based on the uap repository as published in Kämpf, C., Specht, M.,Scholz, A. et al. uap: reproducible and robust HTS data analysis. BMC Bioinformatics 20, 664 (2019), which is located here.

This version v2.0.0rc2 contains the following changes (for a complete list see the CHANGELOG):

• code conversion from Python2 to Python3
• improved user interaction
• enhanced error detection for configuration
• validation of existing results by using annotation as configuration and recalculation of SHA256
• status --details completely lists errors or changes caused by adaptation of the configuration
• enhanced detection of changes (software version, output files, sha256 of results (optional))
• improved error-management
• removed checksum suffix in output directories
• extended backward-compatible connection-management
• Source_controller step to check input data
• no need to configure uap internal scripts, GNU coreutils and lmod
• improved job-execution (signal handling, array jobs, enhanced logging, changes to configuration do not impact running jobs)
• processes are executed in temporary directories
• error fixing and code improvement

Please note, the version v2.0.0rc2 of uap requires Python >= 3.5 and is only tested on SLURM.

Singularity Container

A singularity container that encapsulates uap can be found in our Sylabs registry. Within this container, we provide uap with support for SLURM and UGE grid engines.

• uap.sif:latest mirrors this commit: f0d2cc2

Contacts

• Christoph Kämpf, christoph.kaempf@izi.fraunhofer.de
• Kristin Reiche, kristin.reiche@izi.fraunhofer.de
• Jana Schor, jana.schor@ufz.de
• Jörg Hackermüller, joerg.hackermueller@ufz.de
• Sebastian Canzler, sebastian.canzler@ufz.de

Helmholtz Centre for Environmental Research - UFZ
Permoserstr. 15, 04318 Leipzig, Germany

Fraunhofer Institute for Cell Therapy and Immunology (IZI)
Perlickstraße 1, 04103 Leipzig, Germany

Main contributors:

• Christoph Kämpf
• Dominik Otto
• Michael Specht
• Alexander Scholz
• Sven-Holger Puppel
• Gero Doose
• Kristin Reiche
• Sebastian Canzler
• Julienne Lehmann
• Jana Schor
• Jörg Hackermüller

License

Copyright (C) 2011 - 2020 Helmholtz Centre for Environmental Research - UFZ and Fraunhofer Gesellschaft zur Foerderung der angewandten Forschung e.V. acting on behalf of its Fraunhofer Institute for Cell Therapy and Immunology (IZI).

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the UFZ-IZI License document for more details.