We are working with some very large sequence libraries (paired end 70M reads+ each end - 15Gbx2). We already know what the file types are and that they are appropriate for the  pipeline. There seems to be a large amount of the processing effort expended after the completion after each step in the workflow  analysing the files and determining their attributes - this is related to the size of the files (which are large at every step) and is of no practical use to us, except maybe on the final step.

Is there any way to suppress post processing steps and simply accept the file as specified in the tool output tags? If not would there be any unexpected implications if we revise the scripts and remove any of these steps? Which scripts should we focus on?

Cheers