I want use deepbinner as the first step of a workflow. Deepbinner scans fast5 files for barcodes and then moves them to different folders accordingly. My problem is that files are sorted into a temp directory created by cwltool and disappear from their original location. The temporary files are then processed further and i get my desired output. However, all my raw data is lost.
Is there a way to prevent this behavior? I would like for the workflow to not alter the input directory at all, but i don't know how to make sure deepbinner only gets a copy of the directory.