Documentation request: Better examples of the inputs to ExtractIlluminaBarcodes, IlliminaBasecallsToFastq, and IlluminaBasecallsToSam

[bkohrn]

Documentation request

Tool(s) involved

ExtractIlluminaBarcodes (option BARCODE_FILE), IlliminaBasecallsToFastq (option MULTIPLEX_PARAMS), and IlluminaBasecallsToSam (option LIBRARY_PARAMS)

Description

It would be useful if there were a few more well-formatted examples of each of these files in the documentation, including examples of formatting them using multiple index sequences while still retrieving the unknown index reads. As it stands, it is not clear how these files relate to each other, or to the sample sheet initially provided to the sequencer, nor is it clear how to format the second+ barcode when trying to output unknown reads.

Alternatively (feature request), have a way to automatically parse the information in these files from the Illumina sample sheet without needing the user to parse it by hand.