Added project name to the output directories of the processes.  Now the output directories are Project-name_Sample-key_Date.
Thought about it some more.  The SampleQsubProcess should only be linked to sample_key, so I removed the project name from the output directory here.  Also, the project name should be linked to the barcode, not the sample key, so I transfered that info.  Also, instead of having the Standard and QualityControl Pipelines linked to a flowcell, they should be linked to a barcode.  This allows a natural way to pull out the project info for these pipeline (I'll just have to write a new pipeline when I want to pull fastq from multiple sequencing runs --- duh.  I've implemented all of these changes.
Added colors by lane for the current flowcell for the plots.
Ran a debugged the pipeline up to bcbio.  Need to look into databases to make sure nothing is being eroneously created, but it seems to work otherwise (jobs submitted properly and tracked.)
Debugged the later scripts to make the pngs work.  Also handled some other small bugs.  Introduced new logic for complete.
Debugged the reports some more.  Now running another RapidRun flowcell to check.
Began to add pdf_wrapping, but want to work off the cluster.