Add alignment files
Modify file classification to include alignment files
Add alignment files to pre -> casava transfer
Only add fastq.txt files to files
Default log path now under a2010002; switched command-line argument order for sample_delivery_note.py
Merge pull request #13 from guillermo-carrasco/master

Unittest dependency
Add functionality for clean operation
Update tests
Update docs
modified to use Casava 1.8+ headers
Merge branch 'master' of github.com:SciLifeLab/scilifelab
Merge pull request #14 from b97pla/master

Update to use Casava1.8+ fastq headers
Run command now in bcbio controller
Add query yes no to run
Sample naming issues
Add check for files; if pipeline has started, it unzips zipped files. Change extension if files not found
Merge branch 'feature/pm' of github.com:percyfal/scilifelab into feature/pm
Bug fix related to rounding
Adds customer reference from ProjectSummary document
added parseable arguments