Ensure pipeline version is put into output

[necrolyte2]

Currently there is no way to see what version of the pipeline was used for a given project.
When the pipeline runs, it should just simply echo the metadata.version somewhere

[averagehat]

We could also save a copy of the parameter file, that would give all the information to even re-run the pipeline.

[necrolyte2]

The param file is in the input directory already