config file

Using a config file

Config files are a reproducible way to ensure that the same parameters are shared each time a workflow is run. It is common to specify paths to databases and solidify parameter values in config files.

To get a copy of a template config file with every editable parameter, run the following command

nextflow run UPHL-BioNGS/Grandeur --config_file true

This will create a config file named edit_me.config into the End User's current directory. This file can be renamed and edited without altering the original workflow. The parameters (also known as params) in this file are all preceded by //, which indicates that they are not in use. The // must be removed for that line to be taken into consideration from the workflow.

To use this config file during runtime, simply specify the config file with -c on the command line.

nextflow run UPHL-BioNGS/Grandeur -c edit_me.config

This master config file can also be found at Grandeur/configs/grandeur_template.config.