#From a set of fastq files, will provide QC and read count

$order
1=fastqc
2=cutadapt
3=tophat2
4=picardToolsSortSam
5=htseqcount

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

$cutadapt
-O=10
-m=35
-q=20
--overlap=7
-u=8
-U=8
# Adaptator1 is removed in the forward (-b) and reverse (-B) reads (5' and 3' position)
-b ADAPTATOR1REVERSE -B ADAPTATOR1REVERSE
# Same traitement is done for the forward adaptator sequence
-b ADAPTATOR1FORWARD -B ADAPTATOR1FORWARD


$tophat2
-i=30
-I=20000
-a=8
-m=1
--no-coverage-search
-g=10
--bowtie-n
--library-type=fr-unstranded
--microexon-search

$htseqcount
-r=name
-s=no
-t=mRNA
-m=union
-i=ID

$picardToolsSortSam
SORT_ORDER=coordinate
VALIDATION_STRINGENCY=SILENT
CREATE_INDEX=TRUE