##############################################################################################################
## ClinQC Options file (ClinQCOptions.txt)
##
## Note: This configuration file is used when user has expression data for parent1, parent2 and F1.
##
## This file sets the customizable options for running ClinQC. The options include the paths to the
## database cross reference files, paths to executables, annotation files and other parameters of the pipeline
##
## This file contains example parameter settings, which can be used to run the test data set
## provided with ClinQC. 
## For running ClinQC with your own data, the example parameter values have to be modified.
## Please note that only the input value but not the parameter name itself should be changed.
##
## Note: 1) Lines starting with # are comment lines. They do not need to be changed.
##       2) Parameter's name is case sensitive. The parameters can be changed
##          by replacing the values after the Ò=Ó sign.
##
##############################################################################################################


# Output directory: the name of the directory can be changed.

#OUTPUT_DIRECTORY = /ClinQC_1.0/sanger_output
OUTPUT_DIRECTORY = test_output/sanger_test

# Give the number of processors that should be used in ClinQC pipeline.
THREAD = 10


### Sequencing data quality and trimming parameters
Minimum_Base_Quality = 20
Minimum_Read_Length = 50
Maximum_Read_Length = 1000




### Sanger data quality control and trimming parameters for TTUNER
Sanger_Trim_Window_Size = 10
Sanger_Trim_Base_Quality = 20



##################################################################################################################################
#
#                                       Provide the experiment information files
#
##################################################################################################################################

### Target_File contains Sequencing information. (Mandetory)
Target_File = test_data/sanger/scf/test_target_file.txt
#Target_File = test_data/sanger/ab1/test_target_file.txt


### Provide the Primer and adapter sequences for trimming
#Primer_Adapter_File = test_data/sanger/ab1/adapter_primer_sanger.txt




##############################################################################################################
#
# Third party software/tool executables
# Provide the full path to the third party executables to run the ClinQC pipeline.
#  
#
##############################################################################################################

###### FASTQC executables
#FASTQC = ClinQC_1.0/executables/FastQC/fastqc
FASTQC = executables/FastQC/fastqc

###### Sanger base calling tool
#TTUNER = ClinQC_1.0/executables/tracetuner_3.0.6beta/rel/Linux/ttuner
TTUNER = executables/tracetuner_3.0.6beta/rel/Linux_64/ttuner

##### AlienTrimmer is used to trim the additional sequences (Adapters and Primers) and Homopolymers
#AlienTrimmer = ClinQC_1.0/executables/AlienTrimmer_0.4.0/src/AlienTrimmer.jar
AlienTrimmer = executables/AlienTrimmer_0.4.0/src/AlienTrimmer.jar