Using Broad Institute RNAseq pipeline
You need to follow the readme of this folder to  use the pipeline, there you will find instructions about how to align, mark duplicates, quantificate, and aggregate the results.

If you want to execute the WDL scripts you can follow this guide using Cromwell. Basically use: java -jar Cromwell.jar run myWorkflow.wdl --inputs myWorkflow_inputs.json