Define where the pipeline should find input data and save output data.
Options required to basecall and demultiplex samples.
Options to adjust parameters and filtering criteria for read alignments.
Options to adjust quantification and differential analysis
Options to skip various steps within the workflow.
Options for the reference genome indices used to align reads.
Less common options for the pipeline, typically set in a config file.
Set the top limit for requested resources for any single job.
Parameters used to describe centralised config profiles. These should not be edited.