Define where the pipeline should find input data and save output data.
Options for processing reads with unique molecular identifiers
Options for filtering reads prior to alignment
Reference genome related files and options required for the workflow.
Options to adjust read trimming criteria.
Options to adjust parameters and filtering criteria for read alignments.
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.