Define where the pipeline should find input data and save output data.
Options for the reference genome indices used to align reads.
Parameters for Hi-C data processing
Options to call significant interactions
Options to build Hi-C contact maps
Skip some steps of the pipeline
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.