This repository contains the Collection of Hierarchical UMII-RIS Pipelines (CHURP).
If you use CHURP in your research, please cite our paper from Practice and Experience in Advanced Research Computing (PEARC) 2019:
Joshua Baller, Thomas Kono, Adam Herman, and Ying Zhang. 2019. CHURP: A Lightweight CLI Framework to Enable Novice Users to Analyze Sequencing Datasets in Parallel. In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning) (PEARC ’19). Association for Computing Machinery, New York, NY, USA, Article 96, 1–5. DOI:https://doi.org/10.1145/3332186.3333156
This software package was developed by the Research Informatics Solutions (RIS) group at the Minnesota Supercomputing Institute, with funding provided by the University of Minnesota Informatics Institute (UMII).
For help with using the pipelines, please see the Wiki of this repository. If your issue is not resolve there, please file a new issue on this repository, and we will troubleshoot the issue. If you are running this software on MSI systems, you can contact the MSI help desk at help [@] msi.umn.edu. If you contact the MSI help desk, be sure to include CHURP in the subject line, and please include the command you ran, the samplesheet.txt file, the pipeline.sh file, and a description of the error you are encountering.
The following pipelines have been implemented:
- Group template generation for bulk RNAseq
- Bulk RNAseq
The current version is 1.0.1, released on 2024-07-23.
To gain access to a development version, with experimental new features and bug fixes, see the other branches in this repository. Be warned that development versions are highly unstable and not tested for accuracy; you should only use a development version if you are familiar with Python package development and RNAseq analysis "by hand." We do not support issues arising from a development version of CHURP.
If you need to use an older version of the pipelines to reproduce an analysis, you may download them from the "Releases" section of this repository.