Define where the pipeline should find input data and save output data.
Reference genome related files and options required for the workflow.
Options to adjust adapter trimming criteria.
Options to adjust parameters and filtering criteria for read alignments.
Options to adjust peak calling criteria.
Options to adjust differential analysis criteria.
Options to skip various steps within the workflow.
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.