Edit run_pipelines

[cwtyson]

I made a few small changes to run_pipelines

The main types of changes were:

• Added dplyr::ungroup within each chunk that combines the data frames from each pipeline. This is helpful since if the input data has some grouping structure, it will create duplicate row numbers and this isn't helpful for the quality checks.
• Add namespaces where missing.
• Changed some of the linebreaks
• Added a missing underscore to the beginning of the 'Individual_data' output filename

Nothing of major importance, but hopefully still helpful.

[cwtyson]

I didn't realize that this wasn't branched from the master, so there are many more commits here than I intended to merge...