Define where the pipeline should find input data and save output data.
Adjust parameters and filtering criteria for read alignments.
Reference genome related files and options required for the workflow.
Adjust trimming criteria and sequences.
Control the ribosomal RNA removal through SortMeRNA.
Define parameters for paraclu clustering.
Skip various steps within the 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.