Code for running multiple lanes

[leeanapeters]

Hi, thank you for this great package!

I realized when I first ran this pipeline I only used one lane, when my data are spread across 2 lanes. However, when I try to include multiple lane fastqs I get an unrecognized argument error even though I have version 1.4.5 installed which should be able to handle multiple fastqs.

I can't find documentation as to if there is a different script to run files this way. I was just using -R1 path1 path2 -R2 path1 path2
Should I be doing something different?

Thanks

Leeana