Demultiplexing NovaSeq with samples having different sequencing cycles

Question

[pacman]

Our lab recently switched to NovaSeq from Hiseq which leads to having samples from multiple experiments sequenced with different read parameters in the same run. Right now, I make SampleSheet for every read parameters and run bcl2fastq for each of them which is both time and space consuming ( I have to constantly delete Undetermined fastq) . I was wondering if anyone has a better approach to deal with a mixed-read run.

[GenoMax]

Have you tried to use lane specific --use-bases-mask or are you running mixed pools on all lanes?

samples from multiple experiments sequenced with different read parameters in the same run.

That is not making a lot of sense. Run parameters for whole run must be constant since you need to decide them upfront. I assume you mean that you set cycles required for the longest sample pool and then process the data multiple times to get all other samples? Are you also mixing 1D and 2D index containing pools?