Define where the pipeline should find input data and save output data.
Experimental protocol used to generate the data
Define the paths to the igblast and IMGT databases if you have them cached.
Define the primer region start and how to deal with the primer alignment.
Define how UMI barcodes should be treated.
Options for adapter trimming and read clipping
Options for the presto tools
Define how the B-cell clonal trees should be calculated.
Define downstream analysis options.
Options for software packaging
Options for the reference genome indices used to align reads.
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.
Arguments for this subworkflow