Hello all! I have a general question about the scrnaseq pipeline. I noticed that the BAM files that were output as part of this pipeline were not indexed. I was wondering if there's a way I can add a step (such as "samtools index") that would output the BAI files along with the BAM files? Would this be a simple config file change or something a bit more difficult? Any help is much appreciated!

I think there is no such option currently, but it would not be too hard to add. But also the gain is not huge, as generating the indices should not take too long outside the pipeline. What aligner are you using? Then I could maybe give you some guidance on how to get this working