3. Setup projects with RUMP using local machine

Direct to the RUMP folder. (<1s)

replace /ufrc/djlemas/xinsongdu/jupyter_notebook/projects/RUMP/ with the location on your own machine

cd /ufrc/djlemas/xinsongdu/jupyter_notebook/project/RUMP/

Execute RUMP with provided sample data. (8h for default configuration)

nextflow main.nf -profile docker --input_dir_pos functional_test/sample_data/POS/ --input_dir_neg functional_test/sample_data/NEG --POS_design_path functional_test/sample_data/pos_design.csv --NEG_design_path functional_test/sample_data/neg_design.csv

Execute RUMP with provided sample MZmine outputs. (1m)

Sample outputs of MZmine are provided directly, and processes regarding using MZmine to process raw data, which are the most time-consuming processes, will be skipped.

nextflow run_aftermzmine.nf -profile docker --input_dir_pos functional_test/sample_data/POS/ --input_dir_neg functional_test/sample_data/NEG --POS_design_path functional_test/sample_data/pos_design.csv --NEG_design_path functional_test/sample_data/neg_design.csv --pos_mzmine_peak_output functional_test/sample_results/peak_table/pos_data_before_blank_subtraction.csv --neg_mzmine_peak_output functional_test/sample_results/peak_table/neg_data_before_blank_subtraction.csv

Use RUMP to process your own data. (See executing time estimation)

1. Save your positive data files (.mzXML format) to data/POS/ and negative data to data/NEG/
2. Create design files for positive data and negative data, indicating the group of each file, save them to data/pos_design.csv and data/neg_design.csv. Sample design file can be found in data/sample_data/pos_design.csv and data/sample_data/neg_design.csv
3. Execute RUMP

nextflow main.nf -with-docker xinsongdu/lemaslab_rump:v1.0.0