hi! just wondering how the bowtie index path is specified. I tried: "bwt2_index": "/zfshomes\/aparikh02\/SetupControls\/Genomes\/mouse_m34\/bowtie\/GRCm39" in my params. and that is the correct path. and the bt indices I downloaded are GRCm39.1.bt2 GRCm39.3.bt2 GRCm39.rev.1.bt2 GRCm39.2.bt2 GRCm39.4.bt2 GRCm39.rev.2.bt2. did I do something wrong?

I think now you do not need to put the file prefix ... but just the folder path.

oh oops! thank you