I'm trying to demultiplex several fastq files, each representing a MiSeq lane. I have one metadata file which includes a 'barcodes' column and a 'lane' column.
If I try to demultiplex either lane using q2 demux and the metadata file, it errors out because some barcodes are shared across lanes. I've managed to make it work by creating mapping files for each lane so that barcodes are unique within each file. Is there a more elegant way to accomplish this, ideally within qiime2?