Define where the pipeline should find input data and save output data.
Options required to basecall and demultiplex samples.
Options to adjust parameters and filtering criteria for read alignments.
Options to adjust pameters for DNA varinat calling and structural variant calling.
Options to adjust quantification and differential analysis
Options to adjust the RNA fusion analysis
Options to adjust the RNA modification analysis
Options to skip various steps within the workflow.
Reference genome related files and options required for 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.