Add all required arguments as pipelines inputs

[afrendeiro]

This should ease the requirement to use the pipelines with looper (through the sample yaml).
Passed arguments in command line should overwride any passed in the sample yaml if this is also passed.

[nsheff]

I think that would be great. it decouples looper from pipelines.

[nsheff]

actually I really like this idea...and I think we should make this standard for all the pipelines. Did you ever finish this concept?

This is somewhat related to a new PR #17 that deals with a change in how pypiper args are added.