Does HiCpro overwrite, or skip over previously completed samples?

[Berkley Gryder]

I have good results, but want to run new samples by adding them to the INPUT_DATA directory.  I want to keep the same OUTPUT_DATA directory, hoping that it will not rerun already completed samples.

Does HiCpro overwrite and rerun, or skip over previously completed samples?

[nservant]

Currently, if you try to run HiC-Pro twice on the same output folder, it will ask you if you want to overwrite it.
If you say 'no', the pipeline is not run.
However, this is not true in stepwise mode, but keep in mind that nothing special is done to check if a file already exits, meaning that if two files have the same names, the second one will overwrite the first one.