Perhaps issue an error or warning if no outputs are defined in the CTD?
/home/mcrusoe/miniconda2/envs/ctd-converter/bin/cwltool 1.0.20180130110340
Resolved 'mason_methylation.cwl' to 'file:///home/mcrusoe/src/CTDSchema/seqan/mason_methylation.cwl'
Tool definition failed validation:
mason_methylation.cwl:6:1: Object `mason_methylation.cwl` is not valid because
tried `CommandLineTool` but
missing required field `outputs`