{
  "port": 8000,
  "nextAuthUrl": "https://seqdesk.example.org",
  "nextAuthSecret": "set-via-env-SEQDESK_NEXTAUTH_SECRET-or-replace",
  "anthropicApiKey": "set-via-env-ANTHROPIC_API_KEY-or-replace",
  "adminSecret": "set-via-env-SEQDESK_ADMIN_SECRET-or-replace",
  "databaseUrl": "postgresql://seqdesk:replace-with-password@127.0.0.1:5432/seqdesk?schema=public",
  "directUrl": "postgresql://seqdesk:replace-with-password@127.0.0.1:5432/seqdesk?schema=public",
  "sequencingDataDir": "/data/sequencing",
  "pipelinesEnabled": true,
  "pipelineRunDir": "/data/pipeline_runs",
  "pipelineDatabaseDir": "/data/pipeline_databases",
  "useSlurm": true,
  "slurmQueue": "cpu",
  "slurmCores": 4,
  "slurmMemory": "64GB",
  "slurmTimeLimit": 12,
  "slurmOptions": "--qos=standard",
  "condaPath": "/opt/miniconda3",
  "condaEnv": "seqdesk-pipelines",
  "nextflowProfile": "conda",
  "nextflowWeblogUrl": "https://seqdesk.example.org/api/pipelines/weblog",
  "weblogSecret": "set-via-env-SEQDESK_WEBLOG_SECRET-or-replace",
  "privatePipelines": {
    "metaxpath": {
      "repository": "hzi-bifo/MetaxPath-Nextflow",
      "ref": "main",
      "releaseTag": "latest",
      "packageUrl": "",
      "key": "set-via-env-SEQDESK_METAXPATH_KEY-or-replace",
      "sha256": ""
    }
  },
  "forms": {
    "order": {
      "groups": [
        {
          "id": "group_sequencing",
          "name": "Sequencing Information",
          "description": "Run type and sequencing materials",
          "icon": "Dna",
          "order": 1
        }
      ],
      "fields": [
        {
          "id": "field_run_type",
          "type": "select",
          "label": "Run Type",
          "name": "run_type",
          "required": false,
          "visible": true,
          "helpText": "Experiment type for this sequencing run.",
          "options": [
            {
              "value": "metagenomics",
              "label": "Metagenomics"
            },
            {
              "value": "metatranscriptomics",
              "label": "Metatranscriptomics"
            },
            {
              "value": "other",
              "label": "Other"
            }
          ],
          "order": 10,
          "groupId": "group_sequencing"
        }
      ]
    },
    "study": {
      "groups": [
        {
          "id": "group_study_info",
          "name": "Study Information",
          "description": "Core study context and descriptive information",
          "icon": "FileText",
          "order": 0
        }
      ],
      "fields": [
        {
          "id": "field_study_title",
          "type": "text",
          "label": "Study Title",
          "name": "study_title",
          "required": true,
          "visible": true,
          "order": 1,
          "groupId": "group_study_info"
        }
      ]
    }
  },
  "bootstrap": {
    "users": {
      "admin": {
        "email": "admin@example.org",
        "password": "set-via-env-or-replace-then-change-after-first-login",
        "firstName": "Site",
        "lastName": "Admin",
        "facilityName": "Example Sequencing Facility"
      }
    }
  },
  "site": {
    "name": "Example Sequencing Facility",
    "contactEmail": "support@example.org"
  },
  "auth": {
    "allowRegistration": false
  },
  "access": {
    "departmentSharing": true,
    "allowDeleteSubmittedOrders": false,
    "allowUserAssemblyDownload": true,
    "orderNotesEnabled": true
  },
  "ena": {
    "testMode": true,
    "username": "Webin-XXXXX",
    "password": "set-via-env-SEQDESK_ENA_PASSWORD-or-replace",
    "brokerAccount": false,
    "centerName": "Example Center"
  },
  "telemetry": {
    "enabled": false
  },
  "notifications": {
    "enabled": false
  }
}