Re-design the current pipeline

[Nicklas Nordborg]

The current pipeline is going to be replaced by a new and more modern version, but this is still in the unknown future. The only thing we need to keep is the pilot report so the current pipeline should be redesigned in order to keep as little data as possible to achieve this. This ticket is divided into the following subtickets:

• Merge the Tophat alignment and Cufflinks job to a single job (#983)
• Skip the cufflinks import to the raw data table (#984)
• Re-design the pilot report generator so that it can produce the report using data from the cufflinks file (#985)
• More...??

When all is in place, we probably need to fix the auto-confirm functionality since it will probably not check that correct things for it to be able to proceed.