How to demultiplex a mix of single-indexed and dual-indexed samples
I'm late to the party but simply run cellranger mkfastq twice, with different arguments for the mask and with --filter-dual-index for the double-indexed samples. In a second step you then have to disentangle the dual A+B reads from single-index A reads based on the readID's that are found in both of the demultiplexings. This is cumbersome and time+diskspace consuming, but it can be done. I would use some Unix tools for that but there are probably smarter ways.
EDIT: I mistakenly said bcl2fastq, this must be cellranger mkfastq. (thanks AmadeusDrZaius)