added missing download reference param in example job, update cwltool version
added missing download reference param in example job, update cwltool version

ICGC-TCGA-PanCancer/CGP-Somatic-Docker,ICGC-TCGA-PanCancer/CGP-Somatic-Docker,ICGC-TCGA-PanCancer/CGP-Somatic-Docker,ICGC-TCGA-PanCancer/CGP-Somatic-Docker