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Examples

The most reproducible way to change how the pipeline should run is to use custom Nextflow configuration files.

There are a number of example configuration files here: https://github.com/socialgene/sgnf/tree/main/conf/examples

Use a profile included in SocialGene

To use a built-in configuration file (the ones listed at the link above) use the -profile whichever-profile-i-want flag.

For example, the command below will use the ultraquickstart configuration file (https://github.com/socialgene/sgnf/blob/main/conf/examples/ultraquickstart.config) and run the processes using Docker.

nextflow run socialgene/sgnf -r main \
    -profile ultraquickstart,docker