configExample.json

{
  "_comment": "SBATCH configuration",
  "slurm_header": {
    "time": "12:00:00",
    "threads": "8",
    "qos": "normal",
    "job_prefix": "MLST",
    "project": "production",
    "type": "core"
  },
  "regex": {
    "mail_recipient": "username@suffix.com",
    "_comment": "File finding patterns. Only single capture group accepted (for reverse/forward identifier)",
    "file_pattern": "\\w{8,12}_\\w{8,10}(?:-\\d+)*_L\\d_(?:R)*(\\d{1}).fastq.gz",
    "_comment": "Organisms recognized enough to be considered stable",
    "verified_organisms": []
  },
  "_comment": "Folders",
  "folders": {
    "_comment": "Root folder for ALL output",
    "results": "/tmp/MLST/results/",
    "_comment": "Report collection folder",
    "reports": "/tmp/MLST/reports/",
    "_comment": "Log file position and name",
    "log_file": "/tmp/microsalt.log",
    "_comment": "Root folder for input fasta sequencing data",
    "seqdata": "/tmp/projects/",
    "_comment": "ST profiles. Each ST profile file under 'profiles' have an identicial folder under references",
    "profiles": "/tmp/MLST/references/ST_profiles",
    "_comment": "ST folder. Each references sub-folder contains the .tfa file for each locus of the organism",
    "references": "/tmp/MLST/references/ST_loci",
    "_comment": "Resistances. Commonly from resFinder",
    "resistances": "/tmp/MLST/references/resistances",
    "_comment": "Download path for NCBI genomes, for alignment usage",
    "genomes": "/tmp/MLST/references/genomes",
    "_comment": "PubMLST credentials",
    "pubmlst_credentials": "/tmp/MLST/credentials"
  },
  "_comment": "Database/Flask configuration",
  "database": {
    "SQLALCHEMY_DATABASE_URI": "sqlite:////tmp/microsalt.db",
    "SQLALCHEMY_TRACK_MODIFICATIONS": "False",
    "DEBUG": "True"
  },
  "_comment": "Thresholds for Displayed results",
  "threshold": {
    "_comment": "Typing thresholds",
    "mlst_id": 100,
    "mlst_novel_id": 99.5,
    "mlst_span": 90,
    "motif_id": 97,
    "motif_span": 90,
    "_comment": "Quality Control thresholds",
    "total_reads_warn": 75,
    "total_reads_fail": 70,
    "NTC_total_reads_warn": 10,
    "NTC_total_reads_fail": 20,
    "mapped_rate_warn": 50,
    "mapped_rate_fail": 30,
    "duplication_rate_warn": 20,
    "duplication_rate_fail": 80,
    "insert_size_warn": 140,
    "insert_size_fail": 100,
    "average_coverage_warn": 100,
    "average_coverage_fail": 10,
    "bp_10x_warn": 85,
    "bp_10x_fail": 75,
    "bp_30x_warn": 70,
    "bp_50x_warn": 50,
    "bp_100x_warn": 20
  },
  "_comment": "Genologics temporary configuration file",
  "genologics": {
    "baseuri": "https://lims.facility.se/",
    "username": "limsuser",
    "password": "mypassword"
  },
  "_comment": "PubMLST credentials",
  "pubmlst": {
    "client_id": "",
    "client_secret": ""
  }
}