rsync tricks

Copy Directory Structure and Specific File Types

I wanted to copy over some bams and maintain the directory structure (Sample/bam/Sample.bam) using rsync to preserve timestamps and ownership.

The command I used:

rsync -av  --include='*.bam*' --include='*/'--exclude='*' /path/to/Samples* ./Destination/

This copied the entire directory structure for each sample and the required bam files. I could have excluded the empty directories using --prune-empty-dirs but like to have it just in case.

This stackexchange question was very useful.