Update a Pipeline

[pbelmann]

At the moment a user would have to run two commands in order to update the pipeline.
This is because we are storing our vendor packages (python, virtualenv) in nextflow assets directory.
Therefore a simple nextflow pull metagenomics/MeRaGENE does not work because it reports that
it contains uncommited changes:

nextflow pull metagenomics/MeRaGENE
Checking metagenomics/MeRaGENE ...
metagenomics/MeRaGENE contains uncommitted changes -- cannot pull from repository

I believe there should be an easier way for updating. Maybe we should ask Paolo