#This very complete configuration will start from a set of single end FASTQ files and generates a cleaned VCF while removing intermediate data

$order
1=fastqc
2=cutadapt
3=bwaAln
4=bwaSamse
5=picardToolsSortSam
6=samtoolsflagstat
7=samtoolsview
8=samToolsIndex
9=gatkRealignerTargetCreator
10=gatkIndelRealigner
11=picardToolsMarkDuplicates
1000=gatkHaplotypeCaller
1001=gatkVariantFiltration
1002=gatkSelectVariants

$cleaner
3
4
9

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

$cutadapt
-O=10
-m=35
-q=20
--overlap=7
# Adaptator1 is removed in the forward (-b) read (5' and 3' position)
-b ADAPTATOR1REVERSE
# Same traitement is done for the forward adaptator sequence
-b ADAPTATOR1FORWARD

$bwa aln
-n=5

$bwa samse

$picardToolsSortSam
SORT_ORDER=coordinate
VALIDATION_STRINGENCY=SILENT
CREATE_INDEX=TRUE

$samToolsView
-h
-b
-F=4

$gatkRealignerTargetCreator
-T=RealignerTargetCreator

$gatkIndelRealigner
-T=IndelRealigner

$picardToolsMarkDuplicates
VALIDATION_STRINGENCY=SILENT
CREATE_INDEX=TRUE
REMOVE_DUPLICATES=TRUE

$gatkHaplotypeCaller
-T=HaplotypeCaller
-rf BadCigar

$gatkVariantFiltration
-T=VariantFiltration
--filterName 'FILTER-DP' --filterExpression 'DP<10 || DP>600' --filterName 'LowQual' --filterExpression 'QUAL<30'

$gatkSelectVariants
-T=SelectVariants
-selectType=SNP