config.json.template

{
    "LOCAL": {
      "inputdirs": [
        "/path/to/local/input/directory/1/",
        "/path/to/local/input/directory/2/"
      ],
      "sequencer": "miseq",
      "folderregexmiseq": "\\d{6}_[A-Z0-9]{6}_\\d{4}_\\d{9}-[A-Z0-9]{5}$",
      "folderregexnextseq": "\\d{6}_[A-Z0-9]{7}_\\d{1,}_[A-Z0-9]{9}$",
      "watchfilepath": "CompletedJobInfo.xml",
      "logfile": "logfile.log",
      "sleeptime": 5
    },
    "SERVER": {
      "host": "hostname.com",
      "pemfile": "/path/to/hostname.pem",
      "loginid": "firstname.lastname",
      "outputdirs": [
        "/path/to/remote/output/directory/1/",
        "/path/to/remote/output/directory/2/"
      ]
    },
    "EMAIL": {
      "enabled": false,
      "mailsubject": "[illumina-uploader] {status} miseq data transfer to sabin",
      "mailbody": "Run directory {folderToUpload} {status} transferring to Sabin at {timeOfMail}"
    },
    "PLOVER_EMAIL": {
      "enabled": false,
      "emailurl": "https://emailprovider.com",
      "emailtoken": "secrettoken",
      "mailto": "recipient"
    },
    "MCMS_EMAIL": {
      "enabled": false,
      "authurl": "https://site.com/token",
      "clientid": "client_id",
      "clientsecret": "client_secret",
      "emailurl": "https://site.com/email",
      "mailto": ["user@phsa.ca"],
      "senderemail": "sender_email@phsa.ca"
    },
    "COMMANDS": {
      "rsynccommand": "rsync -artvh -p -e \"{sshformat} -i {pem}\" {chmod} {inDir}/{inFile} {login}@{host}:{outDir}",
      "scpcommand": "scp -i {pem} {inDir}/{filename} {login}@{host}:{outDir}/{filename}",
      "sshnixcommand": "ssh",
      "sshwincommand": "/usr/bin/ssh",
      "chmodcommand": "--chmod=Du=rwx,Dg=rx,Fu=rw,Fg=r,o="
    },
    "DB": {
      "location": "local.db",
      "backupfolder": "backups",
      "foldertable": "folderinfo"
    },
    "SQL": {
      "createtable": "CREATE TABLE {} (folder text, status text, querylastrun text);",
      "checkfolderpresence": "SELECT * FROM {} WHERE folder='{}';",
      "insertfolder": "INSERT INTO {} VALUES ('{}','{}','{}');",
      "getfolderstoupload": "SELECT {} FROM {} WHERE status<>'{}';",
      "markfileindb": "UPDATE {} SET status='{}' WHERE folder='{}';"
    }
  }