Profiles and Configuration

The nextflow.config file

In your workflow folder, you will find a file named nextflow.config that looks like this:

includeConfig 'profiles/standard.config'
includeConfig 'profiles/teoroo2.config'
includeConfig 'profiles/alvis.config'

The nextflow.config file contains detailed specifications about the resources to be used by each process, it can also change default parameters in the workflow. The configuration file separates the definition from that of the workflow itself, which means the same workflow will be runnable on any resources supported by nextflow (from local computer, to HPC computer, to cloud-based platforms). Available options can be found in the nextflow documentation.

In PiNNAcLe, those configurations are always defined as "profiles", so that they can be switched with the -profile name option for nextflow run. PiNNAcLe curates a list of profiles for some of the computational resources we have access to. Those can be good starting points for you to adapt for your own need. You are also welcome to contribute your config if think it will be useful for others.