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Local Workstation

The pipeline runs on any Linux-based system using Singularity. Before running the pipeline, follow the quick start instructions to make sure you have all of the prerequisites installed.

To run the pipeline locally you can use the default standard profile:

./main.nf [arguments]

This is equivalent to specifying the localsingularity profile:

./main.nf -profile localsingularity [arguments]

Alternatively, you can use Docker instead of Singularity to execute the processes by using the localdocker profile:

./main.nf -profile localdocker [arguments]