Add custom_barcodes to the annotationOptions config choices

[JudoWill]

Hello,
I'm working to run some libraries prepped using the Paragon COVID-19 kit on the nanopore. That way we can rapid contact trace on the nanopore weekly, and run larger Illumina batches when its economical, using the same prepped libraries.

Since they've already been barcoded by the Paragon protocol I didn't add any sample-level nanopore barcodes. I'm trying to get the samples to properly demultiplex in Rampart using the illumina barcodes but, there doesn't seem to be a way to pass the custom barcode list to porechop through the annotationOptions config file. Your fork of porechop allows a --custom_barcodes file.fasta (https://github.com/artic-network/Porechop/blob/cc40f6f314ab0a3b94e68a0a2422062264f1da4b/porechop/porechop.py#L224) option but it doesn't look like there's a way to pass this file along.

Any suggestions? It seems silly to fork and create a new adapters.py file when the custom_barcodes option is available.

Really loving the tool BTW!

[rambaut]

You can make a copy of default_protocol/pipelines in your own protocol folder and then modify the demux pipeline with a --custom_barcodes option. Not ideal - and an option in annotationOptions would make sense.