Improve memory usage (and maybe time as well) #85
Description
There are many steps that are followed by a BAM sorting step, since the downstream process requires the BAM file to be sorted or for whichever other reason.
A nice update that would be useful for reducing the size of the work folders and maybe also a bit of a speed-up of the pipeline would be to sort some BAM files already as they are generated either with a pipe or by conditionally adding an extra command after a previous step.
This would make the outputs smaller and avoid having duplicated files aka 1 unsorted file, 1 sorted by position, 1 sorted by query name. We could at least get rid of the unsorted file reducing the memory usage.
This would probably require creating some custom containers with the right combination of tools.
(I am adding this issue here but feel free to prioritize the others if this is not a major problem)