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Pipeline Workflow to Analyze RTA Base Calling Data
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  1. Pipeline Workflow to Analyze RTA Base Calling Data Test Command Checks the syntax and that required data is present /path/to/Pipeline/bin/Gerald.pl config.txt /path/to/RunFolder/Data/Intensities/BaseCalls Builds the run folder structure and generates the MakeFiles /path/to/Pipeline/bin/Gerald.pl config.txt /path/to/RunFolder/Data/Intensities/BaseCalls --make Create MakeFiles cd into the analysis directory Make File is created in the Bustard analysis directory cd /path/to/RunFolder/Data/Intensities/BaseCalls/GERALD_DD_MM_YYYY_username Execute MakeFiles Starts the Pipeline run nohup make –j<n> recursive

  2. Pipeline Workflow to Analyze RTA Intensity Data Test Command Checks the syntax and that required data is present /path/to/Pipeline/bin/bustard.py --CIF --GERALD=config.txt /path/to/RunFolder/Data/Intensities Builds the run folder structure and generates the MakeFiles /path/to/Pipeline/bin/bustard.py --CIF --GERALD=config.txt /path/to/RunFolder/Data/Intensities --make Create MakeFiles cd into the analysis directory Make File is created in the Bustard analysis directory cd /path/to/RunFolder/Data/Intensities/Bustard1.4.0_DD-MM-YYYY_user Execute MakeFiles Starts the Pipeline run nohup make –j<n> recursive

  3. Pipeline Workflow to Analyze Images Test Command Checks the syntax and that required data is present /path/to/Pipeline/bin/goat_pipeline.py --GERALD=config.txt /path/to/RunFolder/Images Builds the run folder structure and generates the MakeFiles /path/to/Pipeline/bin/goat_pipeline.py --GERALD=config.txt /path/to/RunFolder/Images --make Create MakeFiles cd into the analysis directory Make File is created in the Bustard analysis directory cd /path/to/RunFolder/Data/C1-NN_Firecrest1.4.0_DD_MM_YYYY_user Execute MakeFiles Starts the Pipeline run nohup make –j<n> recursive