Please let me know if there's a better way to communicate suggested updates. Wiki: https://www.synapse.org/#!Synapse:syn2813589/wiki/401466 The example for RSEM should be: SMC-RNA-Challenge/script/dream_runner.py test dryrun1 SMC-RNA-Challenge/SMC-RNA-Examples/workflow/smcIsoform-rsem-workflow.cwl isoform (script not scripts, and include parent directory name 'SMC-RNA-Challenge' for both paths, not just one). Under github SMC-RNA-Challenge/install-ubuntu.sh should include sudo docker pull dreamchallenge/smcrna-functions (currently missing sudo and breaks)