Define where the pipeline should find input data and save output data.
Reference genome related files and options required for the workflow.
Options for trimming reads and primers.
Options to remove contamination from the reads.
Switches to skip specific pipeline steps, if desired.
Parameters used to describe centralised config profiles. These should not be edited.
Set the top limit for requested resources for any single job.
Less common options for the pipeline, typically set in a config file.