freeze code prior to file restructure

This is to freeze the code before it gets restructured to be able to install with pip.

What's Changed

• improved pipeline.yml documentation by @deevdevil88 in #7
• update panpipes branch to match development branch by @crichgriffin in #6
• X_scVI read in by @crichgriffin in #4
• Crg compat with panpipes dev by @crichgriffin in #10
• updating with sc_pipeline_muon_dev by @crichgriffin in #13

@crichgriffin merged in @bio-la's code to the repo

Full Changelog: 0.1.0...0.1.1