Define where the pipeline should find input data and save output data.
Presets for working with specific bisulfite library preparation methods.
Options for the reference genome indices used to align reads.
Bisulfite libraries often require additional base pairs to be removed from the ends of the reads before alignment.
Parameters specific to the Bismark workflow
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.