adding new software to babraham package: Trim Galore! will be used to trim FASTQ
files for quality and adapters.
adding read trimming functionality to Illumina plugin
Merge branch 'develop' into illuminaUpdate

Conflicts:
	plugins/illumina/src/main/java/edu/yu/einstein/wasp/plugin/illumina/batch/tasklet/SampleSheetTasklet.java
	plugins/illumina/src/main/java/edu/yu/einstein/wasp/plugin/illumina/batch/tasklet/StageResultsTasklet.java
	plugins/illumina/src/main/resources/flows/wasp-illumina.mainFlow.v1.xml
merge
completion of merge?
merging
Merge branch 'develop' into illuminaUpdate
Merge branch 'develop' into illuminaUpdate
Merge branch 'develop' into illuminaUpdate
added static for output folder names and samplesheets.
check for presence of undetermined_indices folder before copy
check in of work in progress
Merge branch 'develop' into illuminaUpdate
changed instance vars to protected
Merge branch 'develop' into illuminaUpdate
working
Merge branch 'develop' into illuminaUpdate

Conflicts:
	plugins/illumina/src/main/java/edu/yu/einstein/wasp/plugin/illumina/batch/tasklet/PipelineTasklet.java
	wasp-daemon/src/main/java/edu/yu/einstein/wasp/daemon/batch/tasklets/ListenForStatusTasklet.java
removed incomplete redundant file
reverting file, to previous state
Merge branch 'develop' into illuminaUpdate

Conflicts:
	wasp-core/src/main/java/edu/yu/einstein/wasp/filetype/service/impl/FileTypeServiceImpl.java
Merge branch 'develop' into illuminaUpdate

Conflicts:
	wasp-core/src/main/java/edu/yu/einstein/wasp/grid/work/SgeWorkService.java