3  An easy way to set pipeline default parameters

Follow these steps to set default parameters for the pipeline:

1. Download the “params_viafoundry.R” script from GitHub

https://github.com/pipeAIRR/params_viafoundry

2. Create a csv file of pipeline parameters

Create a csv file that contain a table that each row is a parameter you want to defined.

The table columns: - module - the module name - process - the process name - parameter - the parameter name - value - the parameter value

3. Run the script from the command line

Rscript params_dolphinnext.R csv_file.csv

4. Copy output

Copy the text from the file.txt that created to the “Pipeline Header Script” in the “Advanced” tab of the pipeline.