Release 4.0.0

Major Changes

• BAM support
• GDC support: BAM IDs can be supplied via the gdc:// URL
• New tool added: Hera
• Added option to generate workflow inputs derived from users reference genome and annotation files: toil-rnaseq-inputs

Minor Changes

• Added user-defined config option: toil-rnaseq config-input
• Added user-defined manifest option: toil-rnaseq manifest-input
• Added documentation for Auto-scaling on AWS
• Colocated all external dependency code within the repository (except Toil)
• Entire workflow DAG rewritten statically for clarity
• Default workflow inputs supplied in config now open-access
• Switched PyPi pushes to Twine
• Removed BamQC
• Documentation overhaul