Demultiplexing/Run1/analysis/
Demultiplexing/Run1/output/
Demultiplexing/Run2/analysis/
Demultiplexing/Run2/output/
OtherProjects/Run1/analysis/
OtherProjects/Run1/output/
OtherProjects/Run2/analysis/
OtherProjects/Run2/output/

remote_dir="/home/$(whoami)/production"
remote_server="server.org"
production_dir="/data/production"
rsync --dry-run -vrthP -e ssh "${production_dir}/" "$(whoami)"@"${remote_server}":"${remote_dir}/"
--include="Demultiplexing"
--include="Demultiplexing/*/output"
--exclude="*:*"
--exclude="*"