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settings_demo.env
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settings_demo.env
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#### General settings ##############################
TZ=Europe/Copenhagen
####################################################
#### module: Files #################################
QC4METABOLOMICS_module_Files_enabled=TRUE
QC4METABOLOMICS_module_Files_shiny_enabled=FALSE
QC4METABOLOMICS_module_Files_schedule=TRUE
QC4METABOLOMICS_module_Files_file_schedule=FALSE
# matching only these extension (OR). Cannot be empty. Separated by ;
QC4METABOLOMICS_module_Files_include_ext=.mzML;.mzXML;.mzData
# INCLUDE matching full path including filename (AND) Can be empty.
QC4METABOLOMICS_module_Files_include_path=
# EXCLUDE matching full path including filename (OR) Can be empty.
QC4METABOLOMICS_module_Files_exclude_path=WASH;NOQC;MSMS;0000_Test;0000_;_Not OK;DDA
# Read list of files from text file
QC4METABOLOMICS_module_Files_files_from_txt=TRUE
QC4METABOLOMICS_module_Files_files_txt_path=/data/mzML_filelist.txt
QC4METABOLOMICS_module_Files_init_db_priority=1
QC4METABOLOMICS_module_Files_process_order=1
####################################################
#### module: FileInfo ##############################
QC4METABOLOMICS_module_FileInfo_enabled=TRUE
QC4METABOLOMICS_module_FileInfo_shiny_enabled=FALSE
QC4METABOLOMICS_module_FileInfo_schedule=TRUE
QC4METABOLOMICS_module_FileInfo_file_schedule=FALSE
# without extension
# Supported are: instrument, project, mode (if not using below workaround), sample_id
QC4METABOLOMICS_module_FileInfo_mask=%project%_%date%_%instrument%_%batch_seq_nr%_%mode%_%sample_id%
# If you need the mode to be inferred from one of the other fields
QC4METABOLOMICS_module_FileInfo_mode_from_other_field=FALSE
QC4METABOLOMICS_module_FileInfo_mode_from_other_field_which=instrument
QC4METABOLOMICS_module_FileInfo_mode_from_other_field_pos_trigger=LIP1p
QC4METABOLOMICS_module_FileInfo_mode_from_other_field_neg_trigger=LIP1n
QC4METABOLOMICS_module_FileInfo_init_db_priority=2
QC4METABOLOMICS_module_FileInfo_process_order=2
####################################################
#### module: File schedule #########################
QC4METABOLOMICS_module_FileSchedule_enabled=TRUE
QC4METABOLOMICS_module_FileSchedule_shiny_enabled=FALSE
QC4METABOLOMICS_module_FileSchedule_schedule=TRUE
QC4METABOLOMICS_module_FileSchedule_file_schedule=FALSE
QC4METABOLOMICS_module_FileSchedule_init_db_priority=2
QC4METABOLOMICS_module_FileSchedule_process_order=3
####################################################
#### module: TrackCmp ##############################
QC4METABOLOMICS_module_TrackCmp_enabled=TRUE
QC4METABOLOMICS_module_TrackCmp_shiny_enabled=TRUE
QC4METABOLOMICS_module_TrackCmp_shiny_order=1
QC4METABOLOMICS_module_TrackCmp_schedule=TRUE
QC4METABOLOMICS_module_TrackCmp_file_schedule=TRUE
QC4METABOLOMICS_module_TrackCmp_init_db_priority=2
# this needs to be quite large for this strategy to work. Only scans inside this is used AFAIK. The centwave ppm setting will limit appropiately
QC4METABOLOMICS_module_TrackCmp_ROI_ppm=200
QC4METABOLOMICS_module_TrackCmp_findPeaks_method=centWave
QC4METABOLOMICS_module_TrackCmp_findPeaks_snthr=10
QC4METABOLOMICS_module_TrackCmp_findPeaks_ppm=100
QC4METABOLOMICS_module_TrackCmp_findPeaks_peakwidth=3, 18
QC4METABOLOMICS_module_TrackCmp_findPeaks_scanrange=NULL
QC4METABOLOMICS_module_TrackCmp_findPeaks_prefilter=3, 100
QC4METABOLOMICS_module_TrackCmp_findPeaks_integrate=1
QC4METABOLOMICS_module_TrackCmp_findPeaks_verbose_columns=TRUE
QC4METABOLOMICS_module_TrackCmp_findPeaks_fitgauss=TRUE
QC4METABOLOMICS_module_TrackCmp_xcmsRaw_profparam=0
QC4METABOLOMICS_module_TrackCmp_std_match_ppm=100
QC4METABOLOMICS_module_TrackCmp_std_match_rt_tol=20
####################################################
#### module: Contaminants ##########################
QC4METABOLOMICS_module_Contaminants_enabled=TRUE
QC4METABOLOMICS_module_Contaminants_shiny_enabled=TRUE
QC4METABOLOMICS_module_Contaminants_shiny_order=2
QC4METABOLOMICS_module_Contaminants_schedule=TRUE
QC4METABOLOMICS_module_Contaminants_file_schedule=TRUE
QC4METABOLOMICS_module_Contaminants_init_db_priority=2
QC4METABOLOMICS_module_Contaminants_EIC_ppm=100
# only URL implemented
QC4METABOLOMICS_module_Contaminants_cont_list_type=URL
QC4METABOLOMICS_module_Contaminants_cont_list_loc_positive=https://raw.githubusercontent.com/stanstrup/commonMZ/master/inst/extdata/contaminants_%2B.tsv
QC4METABOLOMICS_module_Contaminants_cont_list_loc_unknown=https://raw.githubusercontent.com/stanstrup/commonMZ/master/inst/extdata/contaminants_%2B.tsv
QC4METABOLOMICS_module_Contaminants_cont_list_loc_negative=https://raw.githubusercontent.com/stanstrup/commonMZ/master/inst/extdata/contaminants_-.tsv
####################################################
#### module: Productivity ##########################
QC4METABOLOMICS_module_Productivity_enabled=TRUE
QC4METABOLOMICS_module_Productivity_shiny_enabled=TRUE
QC4METABOLOMICS_module_Productivity_shiny_order=3
QC4METABOLOMICS_module_Productivity_schedule=FALSE
QC4METABOLOMICS_module_Productivity_file_schedule=FALSE
####################################################
#### module: Debug #################################
QC4METABOLOMICS_module_Debug_enabled=TRUE
QC4METABOLOMICS_module_Debug_shiny_enabled=TRUE
QC4METABOLOMICS_module_Debug_shiny_order=5
QC4METABOLOMICS_module_Debug_schedule=FALSE
QC4METABOLOMICS_module_Debug_file_schedule=FALSE
####################################################
#### module: Log ###################################
QC4METABOLOMICS_module_Log_enabled=TRUE
QC4METABOLOMICS_module_Log_shiny_enabled=TRUE
QC4METABOLOMICS_module_Log_shiny_order=4
QC4METABOLOMICS_module_Log_schedule=FALSE
QC4METABOLOMICS_module_Log_file_schedule=FALSE
QC4METABOLOMICS_module_Log_init_db_priority=1
####################################################
#### module: ICMeter ###############################
QC4METABOLOMICS_module_ICMeter_enabled=FALSE
QC4METABOLOMICS_module_ICMeter_shiny_enabled=FALSE
QC4METABOLOMICS_module_ICMeter_schedule=FALSE
QC4METABOLOMICS_module_ICMeter_file_schedule=FALSE
QC4METABOLOMICS_module_ICMeter_init_db_priority=2
QC4METABOLOMICS_module_ICMeter_user=
QC4METABOLOMICS_module_ICMeter_password=
####################################################
#### MS convert settings ###########################
QC4METABOLOMICS_msconvert_args=--filter \"scanEvent 1\" --mzML --zlib --64
QC4METABOLOMICS_msconvert_outdir_prefix=/../mzML
####################################################
#### Internal settings for advanced users ##########
# Do not change unless you know what you are doing
# without trailing slash
QC4METABOLOMICS_base=/data
# database connection
MYSQL_ROOT_PASSWORD=mysql_password
MYSQL_DATABASE=qc_db
MYSQL_USER=qc_db_user
MYSQL_PASSWORD=qc_db_pw
MYSQL_HOST=172.20.0.2
MYSQL_PORT=3306
MARIADB_AUTO_UPGRADE=1
####################################################
#### DB backup #####################################
TIMEZONE=Europe/Copenhagen
CONTAINER_NAME=db-backup
CONTAINER_ENABLE_MONITORING=FALSE
BACKUP_JOB_CONCURRENCY=1 # Only run one job at a time
DEFAULT_CHECKSUM=NONE # Don't create checksums
DEFAULT_COMPRESSION=ZSTD # Compress all with ZSTD
DEFAULT_BACKUP_INTERVAL=1440 # Backup every 1440 minutes/24 h
DEFAULT_BACKUP_BEGIN=+1 # Backup starts immediately
DEFAULT_CLEANUP_TIME=8640 # Cleanup backups after a week
DEFAULT_COMPRESSION=GZ # Compress with GZIP
DB01_TYPE=mariadb
DB01_HOST=172.20.0.2
DB01_NAME=qc_db
DB01_USER=qc_db_user
DB01_PASS=qc_db_pw
####################################################