recover test

.travis/RUMP-test_aftermzmine.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 
 # Test processes MZmine output files with sample data
-./nextflow run_aftermzmine.nf --input_dir_pos .travis/data/POS/ --input_dir_neg .travis/data/NEG --POS_design_path .travis/pos_design.csv --NEG_design_path .travis/neg_design.csv --cutoff 1 --pos_mzmine_peak_output .travis/pos_data.csv --neg_mzmine_peak_output .travis/neg_data.csv -with-docker xinsongdu/lemaslab_rump:v1.0.0
+./nextflow run_aftermzmine.nf --input_dir_pos .travis/data/POS/ --input_dir_neg .travis/data/NEG --POS_design_path .travis/pos_design.csv --NEG_design_path .travis/neg_design.csv --unknown_search 0 --cutoff 1 --pos_mzmine_peak_output .travis/pos_data.csv --neg_mzmine_peak_output .travis/neg_data.csv -with-docker xinsongdu/lemaslab_rump:v1.0.0

.travis/RUMP-test_all.sh

@@ -4,5 +4,5 @@
 wget https://github.com/mzmine/mzmine2/releases/download/v2.53/MZmine-2.53-Linux.zip && unzip MZmine-2.53-Linux.zip && rm MZmine-2.53-Linux.zip
 
 # Test all processes with sample data
-./nextflow main.nf --input_dir_pos .travis/data/POS/ --input_dir_neg .travis/data/NEG --POS_design_path .travis/pos_design.csv --NEG_design_path .travis/neg_design.csv --cutoff 1 -with-docker xinsongdu/lemaslab_rump:v1.0.0
+./nextflow main.nf --input_dir_pos .travis/data/POS/ --input_dir_neg .travis/data/NEG --POS_design_path .travis/pos_design.csv --NEG_design_path .travis/neg_design.csv --unknown_search 0 --cutoff 1 -with-docker xinsongdu/lemaslab_rump:v1.0.0
 

README.md

@@ -3,7 +3,7 @@
 [![travis](https://travis-ci.com/lemaslab/RUMP.svg?branch=master)](https://travis-ci.com/lemaslab/RUMP)
 [![license](http://img.shields.io/badge/license-GNU-blue.svg)](https://github.com/lemaslab/RUMP/blob/master/LICENSE)
 
-# RUMP (Reparing)
+# RUMP
 
 ![alt text](https://github.com/lemaslab/RUMP/blob/master/figs/Metabolomics_Pipeline_V4.png)
 

main.nf

@@ -134,7 +134,7 @@ if (params.help) {
     System.out.println("    --POS_design_path                       location for positive design file, default is 'data/pos_design.csv'")
     System.out.println("    --NEG_design_path                       location for negative design file, default is 'data/neg_design.csv'")
     System.out.println("    --cutoff                                cutoff p-value for mummichog pathway analysis, default is 0.05")
-    System.out.println("    --unknown_search                        whether do unknown search for unidentified metabolites or not, default is '0', please set it to '1' when needed")
+    System.out.println("    --unknown_search                        whether do unknown search for unidentified metabolites or not, default is '1', please set it to '0' when you want to disable it")
     System.out.println("    --version                               whether to show version information or not, default is null")
     System.out.println("    --help                                  whether to show help information or not, default is null")
     System.out.println("Please refer to nextflow.config for more options.")

nextflow.config

@@ -68,7 +68,7 @@ params
     bs = "1"
 
     // Whether do unknown search or not
-    unknown_search = "0"
+    unknown_search = "1"
 
     // Use singularity?
     container = "Docker"
@@ -87,8 +87,8 @@ params
     mzmine_dir = "MZmine-2.53-Linux/"
 
     // Change the following file location (customized library for matching metabolites) to the location on your machine
-    pos_library = "Positive_Garrett_MetaboliteStd_Library_RP_edited01152019JG.csv"
-    neg_library = "Negative_Garrett_MetaboliteStd_Library_RP_edited01152019JG.csv"
+    pos_library = "positive_library.csv"
+    neg_library = "negative_library.csv"
 
     pos_config = "pos_config.xml"
     neg_config = "neg_config.xml"

rump/add_stats.py

@@ -201,7 +201,7 @@ def add_label(row, group1_name, group2_name):
 
 def add_stats(data_file="data_pos_ph.csv", design_file="design", \
               output_file="pos_withstats.csv", \
-              library="Positive_Garrett_MetaboliteStd_Library_RP_edited01152019JG.csv"):
+              library="positive_library.csv"):
     """Add basic statistics to peak table produced by MZmine.
 
     # Arguments:

run_aftermzmine.nf

@@ -124,7 +124,7 @@ if (params.help) {
     System.out.println("    --pos_mzmine_peak_output                location for positive peak table generated by MZmine-2.53, default is 'pos_data.csv'")
     System.out.println("    --neg_mzmine_peak_output                location for negative peak table generated by MZmine-2.53, default is 'neg_data.csv'")
     System.out.println("    --cutoff                                cutoff p-value for mummichog pathway analysis, default is 0.05")
-    System.out.println("    --unknown_search                        whether do unknown search for unidentified metabolites or not, default is '0', please set it to '1' when needed")
+    System.out.println("    --unknown_search                        whether do unknown search for unidentified metabolites or not, default is '0', please set it to '0' when you want to disable it")
     System.out.println("    --version                               whether to show version information or not, default is null")
     System.out.println("    --help                                  whether to show help information or not, default is null")
     System.out.println("Please refer to nextflow.config for more options.")