Reorganize files

Separate RNA-seq pipeline into it's own GitHub repository by renaming the repo to https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL

The original repository was recreated at https://github.com/heliumdatacommons/cwl_workflows

Don't rely on CLASSPATH env variable

Modifications from @mr-c to not rely on the CLASSPATH enviornment variable in markduplicates.cwl.

Use biocontainers, when possible

Updates from @mr-c

• Bypasses wrapper scripts from the gtex-pipeline except for run_rnaseqc.py
• remove threads, memory as specific inputs and derive them from the $(runtime) CWL object instead.
• Use biocontainer, when possible

Initial working RNA-seq CWL workflow

Initial TOPMed RNA-seq pipeline.