############################# public settings #############################
#          Common settings that need to be set for many tools             #
###########################################################################

#Path to the reference genome FASTA file for GRCh38
reference_genome = ""

#Data for lift-over between genome builds (GRCh38 <> GRCh37)
reference_genome_hg19 = ""
liftover_hg19_hg38 = ""
liftover_hg38_hg19 = ""

############################ internal settings ############################
#   If you do not know what these settings mean, leave them unchanged!    #
###########################################################################

#NGSD MySQL credentials
ngsd_host = "localhost"
ngsd_port = 3306
ngsd_name = "ngsd"
ngsd_user = "ngsduser"
ngsd_pass = ""

ngsd_test_host = ""
ngsd_test_port = 3306
ngsd_test_name = ""
ngsd_test_user = ""
ngsd_test_pass = ""

#GL8 MySQL credentials
genlab_mssql = false
genlab_host = ""
genlab_port = 3306
genlab_name = ""
genlab_user = ""
genlab_pass = ""

#megSAP folders
projects_folder_diagnostic = "";
projects_folder_research = "";
projects_folder_test = "";
projects_folder_external = "";
data_folder = ""

#setting for variant scoring/ranking
ranking_variant_blacklist=

#python executable for plotting (set if the python exe is not in the PATH)
python_exe = ""

#NovaSeqX
sample_sheet_path = 
nova_seq_x_sw_version = "4.3.16"
nova_seq_x_app_version = "1.3.13"
nova_seq_x_keep_fastq = 1

#location, used to enable site-specific adaptations
location = ""

#SSL certificate authorities to validate a connection to the database server
db_ssl_ca = ""
