## Configuration file : to generate BAM files from pair-end fastq files using bwa mem, after a QC control of intial data
## http://toggle.southgreen.fr


###############################
# 1 - PIPELINE CONFIGURATION
###############################

#------------------------------
#   Building Workflow
#------------------------------
# After the tag $order define steps composing the pipeline and
# their relative order.
# Each line consists of the step number followed by
# an equal symbol then by the softwareÕs name (e.g. 1=FastQC).
#
# - All the steps with a number <1000
# are carried out for each sample separately
#
# - All the steps with a number > or = 1000
# are performed as a global analysis 
#
# - Step name is not casse-sensitive
#------------------------------

$order
1=fastqc
2=bwa mem
# sort sam
3=picardtoolssortsam 
# get some mapping statistics
4=samtoolsflagstat   
# extracting correctly mapped read
#5=samtoolsview      
#6=samToolsIndex



#------------------------------
#   Providing software parameters
#------------------------------
# Foreach software, parameters can be provided after the line
# composed of the symbol $ followed by the software name 
#
# - If no software parameter provided, the default ones are
# used.
# - TOGGLe will handle itself the input and output files as
# well as the references.
# - see software manual for more details about 
#------------------------------

$bwamem
# put your option

$picardToolsSortSam
SORT_ORDER=coordinate
VALIDATION_STRINGENCY=SILENT
CREATE_INDEX=TRUE

$samToolsView
-h
-b
-f=0x02

###############################
# 2 - DATA MANAGEMENT
###############################

#------------------------------
#   Removing intermediate data
#------------------------------
# users can specify after the tag $cleaner,
# the list of step number (one by line)
#------------------------------

$cleaner
#put the step number that TOGGLe have to manage data 

#------------------------------
#   Compressing data
#------------------------------
# users can specify after the tag $compress,
# the list of step number (one by line) that data have to be compressed
#------------------------------
#$compress


#------------------------------
#   Transferring data from project directory to work directory
#------------------------------
# users can specify after the tag $scp,
# the directory name where the data have to be copied (by scp)
#------------------------------
#$scp
#/scratch




###############################
# 3 - CLUSTER CONFIGURATION
###############################

#------------------------------
#   Setting up jobs scheduler
#------------------------------
#  TOGGLe can run with either LSF, MPRUN, SLURM or SGE
#  jobs schedulers. 
#  - According to the scheduler, after the tag $LSF or $MPRUN or $SLURM or $SGE
#  set scheduler options list
#------------------------------
#Example for SGE
#$sge
#-q YOURQUEUE.q
#-b Y


#------------------------------
#   Providing a specific environment variables
#------------------------------
#  User can specify ENVIRONMENT variables in their jobs (e.g. export or module load)
# using tag $env
#------------------------------
#$env