Can I resume pipeline based on where left off?

[jmpolinski]

Due to memory issues, my pipeline failed during samtools sorting of the files. I was able to sort the files outside of the pipeline and would like to have it resume from that point.

Is resuming from a mid-point possible? How do I make sure it starts after sorting instead of rewriting the files and failing again?

[nservant]

Hi, Please see the -s stepwise mode of HiC-Pro. Basically, you can start running the pipeline from intermediate files. Simply use the same input structure (folder/sample/file) and use the -s option(s) N