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README.md

@@ -5,18 +5,18 @@ Qiime 2 (https://qiime2.org/)
 
 Setup:
 1. Clone the package using "git clone https://github.com/swiftbiosciences/q2_ITS.git" 
-   to get following files: q2wkflow_ITS_v3.sh,  
-   mergeStrand_taxonomy.py, config.txt, primer file, and reference 
+   to get following files: q2wkflow_ITS_ver3.sh,  
+   mergeStrand_taxonomy.py, config_SNAP_ITS.txt, primer file, and reference 
    file (1) for the naive baysian classifier using UNITE ITS reference 
    version 8. 
 
-2. Edit “config.txt” to enter correct absolute paths to each tool, primer 
+2. Edit “config_SNAP_ITS.txt” to enter correct absolute paths to each tool, primer 
    file, and expected read length after primer is trimmed. Set "AS_PE" to 'true'
    if you wish to merge the paired end reads, i.e. R1 and R2, and process the 
    merged reads (recommended for longer read lengths, e.g. 2X250, 2X300).
 
    Command to run:
-   q2wkflow_ITS_v3.sh config.txt inputdir workdir
+   q2wkflow_ITS_ver3.sh config_SNAP_ITS.txt inputdir workdir
 
 3. Results organization: ASV feature table can be found in "Export" directory; 
    "QObj" directory contains intermediate files and tables some of which could 

q2wkflow_ITS_ver3.sh

@@ -2,7 +2,7 @@
 ## Swift Biosciences ITS Qiime 2 workflow
 ## Author Benli Chai & Sukhinder Sandhu 20191009
 ## Remember to edit/set the parameters in config.txt file
-## Run as q2wkflow_ITS.sh config.txt inputDir outputDir
+## Run as q2wkflow_ITS_ver3.sh config.txt inputDir outputDir
 ## make sure output dir exists before running the pipeline
 ## This workflow treats paired-end as single reads or as paired-end reads.
 
@@ -12,7 +12,7 @@ set -x
 
 if [ $# -ne 3 ]
     then
-       echo "q2wkflow_ITS.sh config.txt inputDir workdir"
+       echo "q2wkflow_ITS_ver3.sh config_SNAP_ITS.txt inputDir workdir"
         exit
 fi