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