Layout how parameters are combined

### Description of feature

Parameter for the pipeline have an hierachical order accoring to @jpfeuffer :

If an SDRF file is provided,
1. SDRF parameters - set or no - will of precedence over all other parameters
2. Command line parameters
3. JSON provided parameters

No matter what, my plan is to dump in `pipeline_info` the actual parameters that were used. For parameters that could be sample-specific this might be a challenge (as these cannot be easily aligned fully with the pipeline paramters).

My first aim is to lay out the process in detail in the documentation - and maybe at least ensure that parameters not explicitly set in the SDRF file are picked up from the command line or json file provided parameters.