Elmar Pruesse

There should be a command to 1. Copy out stages to create a static pipeline 2. Copy out stages with custom prefix so they can be altered

When adding e.g. an updated version, a pre-computed spec file will still get installed. Should have some kind of hash in there.

Directly build the {:targets:} of the stage, that way `-f` will also do what it should.

problematic are - `\` (directory separator) - `.` (file type separator, should be ok but could get weird) - `__` (id separator for multiple ids) Could either rewrite those, or...

Copying and modifying a rules-file to the local workflow directory should be possible. Also, add command to do copy stages by name / stagestack (whole file only, I think).

The config has grown complex. It should be validated using a schema definition at startup to make sure nothing weird happens later on. Ideally, that schema would also be used...

Need some minimal dataset to run tests on the RNA Seq rules.