When you have installed and configured the pipeline, prepared the reference genome, and created a design file you can run it with the command below in the top-level directory of the pipeline:
nextflow run main.nf --design <DESIGN_FILE_PATH> --genome <GENOME_NAME> -profile <PROFILE_NAME>You can also specify parameters at the command-line to override those provided in the config files. A list of these can be obtained with:
nextflow run main.nf --helpA template script (run_pipeline.sh) outlining the steps and commands required to run the pipeline is also available to customise.