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Quickstart guide

This guide is for the impatient to get you up and running as quickly as possible. Make sure to read the full guide to learn about all the options that the pipeline exposes.

Choosing a software provisioning framework

GABI provides software on-the-fly. Use whatever profile (-profile) is appropriate for your system:

  • conda
  • apptainer
  • singularity
  • docker
  • podman

We will use -profile apptainer for the examples below. Use a container framework over conda, if at all possible.

Three steps

Follow these three steps to run the integrated test and verify your installation:

Install references

nextflow run marchoeppner/gabi -profile apptainer \
--reference_base /path/to/references \
--build_references \\
--run_name build
-r main

This will download and install the pipeline references to /path/to/references (choose an appropriate path here).

Run test

nextflow run marchoeppner/gabi -profile apptainer,test \
--reference_base /path/to/references \
-r main

The integrated test simply downloads a set of Illumina WGS reads from ENA and assembles them.

Step three

There is no step three. Continue with our full user guide, read more about the outputs and also make sure to double-check the installation guide to learn how to set up a more specific profile for your local system.