This is a small tool that renames files based on sheet of old and new file names (".rename sheet").
This was specifically designed and tested for the iRODS data management system used at the RIVM. The .rename sheet should be saved in the sample sheet directory, similar to the .exclude files for the Juno pipelines.
Any file in the old input collection which is not listed in the first column of the .rename sheet is copied as-is to the new collection. This script does this by copying the directory over the the new directory, and moving files within the new directory as instructed in the .rename file.