#IGV settings
igv_app=
igv_menu=@Invalid()
igv_host=127.0.0.1
igv_port=60151
igv_genome=1kg_v37
igv_virus_genome = ""

#NGSD functionality
NGSD_enabled=true
email_run_finished=""
email_run_analyzed=""

#Clinvar upload
clinvar_api_key=

#Analysis steps for queuing
analysis_steps_single_sample=ma - mapping, vc - SNV/InDel calling + annotation, cn - CNV calling + annotation, sv - SV calling + annotation, re - repeat expansion calling, db - database import
analysis_steps_multi_sample=vc - SNV/InDel calling + annotation, cn - CNV calling + annotation, sv - SV calling + annotation, db - database import
analysis_steps_trio=vc - SNV/InDel calling + annotation, cn - CNV calling + annotation, sv - SV calling + annotation, db - database import
analysis_steps_somatic=vc - variant calling, vi - virus detection, cn - copy number calling, an - annotation, msi - microsatellite instabilty, an_rna - RNA annotation, db - database import
analysis_steps_single_sample_rna = ma - mapping, rc - read counting, an -annotation, plt - plot, fu - fusion, db - database import
analysis_steps_cfdna=ma - mapping, vc - SNV/InDel calling + annotation, db - database import
analysis_steps_single_sample_lr=ma - mapping, vc - SNV/InDel calling, cn - CNV calling, sv - SV calling, re - repeat expansion calling, an - annotation, db - database import
analysis_steps_trio_lr=vc - SNV/InDel calling, cn - CNV calling, sv - SV calling, an - annotation, db - database import
analysis_steps_multi_sample_lr=vc - SNV/InDel calling, cn - CNV calling, sv - SV calling, an - annotation, db - database import

#webservice URLs
PrimerDesign = ""
alamut_host = ""
alamut_institution = ""
alamut_apikey = ""

#proxy settings for GSvar
proxy_host = ""
proxy_port = 
proxy_user = ""
proxy_password = ""

#special folders for GSvar
gsvar_report_folder = ""
gsvar_report_archive = ""
gsvar_xml_folder = ""
gsvar_publication_folder = ""
gsvar_variantsheet_folder = ""
gsvar_variant_export_folder = ""
burden_test_files = ""

#debugging
debug_mode_enabled=false

#somatic data transfer to MTB/QBIC
mtb_xml_upload_url = ""
qbic_data_path = ""

#Number of threads to used for calculations that can be done in parallel (coverage, etc)
threads = 4

#misc settings
build = "hg38"
custom_menu_small_variants = ""
use_free_hgmd_version = false
allow_report_with_all_types = false
gsvar_file_outdated_before = 2021-12-01

#Path to the file that includes root and intermediate certificates, needed to access BAM files over HTTPS
curl_ca_bundle = "ca-bundle.crt"

#Check for the user notifications comming from the server (e.g. information about updates)
display_user_notifications = true
