#This config file will allow users to identify structural variants from a set of fastq files using breakdancer and bwa mem

$order
1=fastqc
2=bwa mem
3=picardtoolssortsam
1000=breakdancer

$picardToolsSortSam
SORT_ORDER=coordinate
VALIDATION_STRINGENCY=SILENT
CREATE_INDEX=TRUE

#PUT YOUR OWN SCHEDULER CONFIGURATION HERE
#Example for SGE
#$sge
#-q YOURQUEUE.q
#-b Y