SciLifeLab/bcbb — pull request #273 by guillermo-carrasco (2013-07-08 14:31:48+00:00)
Title: Custom output path demultiplexing results

This PR adds the necessary changes to be able to specify the output directory for the demultiplexing and BCL to FASTQ conversion. This arises from the problems that we've been having lately when processing in MooseFS. As accorded with @b97pla, the functionality work as follows:

* In the ```transfer_info.yaml``` configuration file, we specify the output directory and if we want to process everything at once or not (necessary if processing in a different directory that the original one, otherwise it may result in b5 and galerina doing half of the calculations).
* ```illumina_finished_msg.py``` will redirect the output of the conversion to the specified folder, or to the default if is not specified.

I also added a flowchart of ``illumina_finished_msg.py`` that I made.