xinsongdu/lemaslab_rump repository overview

A Reproducible Pipeline for Untargeted Metabolomics Data Analysis.

⁠Licence

This program is released as open source software under the terms of MIT License⁠.

⁠Usage

Please refer to our wiki⁠ for how to install and use RUMP

⁠Help message

RUMP can display usage information on the command line:

Nextflow main.nf --help true

⁠Components

RUMP accepts .mzXML and .mzXL files. Files are processed in parallel using MZmine-2.53⁠; several statists are calculated using Python3⁠ codes; interactive report is generated with MultiQC⁠; pathway analysis are done with mummichog⁠; unknown metabolites search are done with CEU Mass Mediator⁠. Note that the processes related to unknow search with CEU Mass Mediator is turned off by default due to the unstable server, it can be turned on by setting parameter --unknown_search to "1".

⁠Currently included statistical analysis

• Student t-test: Test if there is a significant statistical difference of certain peak intensities between the two groups of samples.
• Venn diagram: Report the number of peaks that are significantly enriched in one of the groups, and the number of peaks that have no significant difference between two groups.
• Principal component analysis: Dimensional reduction using the peak intensities of the two group samples, and visualize the difference.
• Hierarchical clustering: Cluster all samples and plot a heatmap to show the difference between samples and peaks.
• Bar plot: plot the metabolites with top-10 and bottom-10 fold-change for the comparison between two groups. (note: the figure will display abnormally if there is an infinite fold change value)

⁠Logging

Logs and error reports will be stored under logs/ folder after running.

⁠Clean repository

Run the following command to clean all the files generated by Nextflow

bash clear.sh

⁠Exit status values

RUMP returns the following exit status values:

• 3: Positive file groups are not the same as negative file groups, please check design files.
• 4: Not all input files are in .mzXML format, please check input data folders.
• 5: One or more input files does not exist.
• Other Linux reserved exit codes⁠

⁠Bug reporting and feature requests

Please submit questions, bug reports and feature requests to the issue tracker on GitHub:

RUMP issue tracker⁠

⁠References

• SECIM Core⁠ provided valuable guidance related to parameter settings of data processing.
• Sample data is from Metabolomics Workbench PR000188⁠
• Data used for continuous integration is from Metabolights MTBLS146⁠