RENEE: Rna sEquencing aNalysis pipElinE

New features

• Support hg38 release 45 on biowulf & FRCE. (#127, @kelly-sovacool)
• hg38 genome index files now include decoy & virus sequences. (#136, @kelly-sovacool)
  • Additionally, --genome is no longer required and is set to hg38_36 by default.
• Set default shared singularity SIF directory for biowulf and frce. (#94, @kelly-sovacool)
• Add renee gui subcommand to launch the graphical user interface. (#94, @kelly-sovacool)
  • Previously, renee_gui (with an underscore) was a command in the ccbrpipeliner module.

Bug fixes

• Ensure renee build creates necessary config directory during initialization. (#139, @kelly-sovacool)
• Run rsem-generate-data-matrix to create gene and isoform matrix files. (#149, @kelly-sovacool)
• Fix bug in the driver script that caused the snakemake module not to be loaded on biowulf in some cases. (#154, @kelly-sovacool)

Documentation updates

• Minor documentation improvements. (#132, #135, #152, @kelly-sovacool)
• Add GUI instructions to the documentation website. (#38, @samarth8392)
• The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#150, @kelly-sovacool)
• Show the name of the pipeline rather than the python script for CLI help messages. (#131, @kelly-sovacool)
• Added Expected output tab to the documentation website and updated FAQs (#156, @samarth8392)