Nxclinical Uploder

The workflow JSON

Copy or download the full n8n JSON below. Paste it into a new n8n workflow, add your credentials, activate. Full import guide →

{
  "updatedAt": "2026-06-19T13:25:34.671Z",
  "createdAt": "2026-06-01T08:05:32.731Z",
  "id": "9z4hRpQRHcHn1c2K",
  "name": "Nxclinical_uploder",
  "active": false,
  "isArchived": false,
  "nodes": [
    {
      "parameters": {},
      "type": "n8n-nodes-base.manualTrigger",
      "typeVersion": 1,
      "position": [
        -432,
        -80
      ],
      "id": "d564bb05-b118-4bc3-af13-14b7f5936ad1",
      "name": "When clicking \u2018Execute workflow\u2019"
    },
    {
      "parameters": {
        "operation": "executeQuery",
        "query": "SELECT \n  doa.uniqueref AS operation_ref,\n  doa.idat_ref,\n  dor.uniqueref AS recipe_ref,\n  dor.account_id,\n  dor.pipeline_id\nFROM data_operations_array doa\nJOIN data_operation_recipes dor ON dor.uniqueref = doa.recipe_ref\nWHERE doa.status_concept_ref = 24\nAND dor.type_concept_ref = 251\nORDER BY dor.uniqueref, doa.uniqueref;",
        "options": {}
      },
      "type": "n8n-nodes-base.postgres",
      "typeVersion": 2.6,
      "position": [
        -224,
        -80
      ],
      "id": "ab8373ee-c826-496f-aaeb-1ad0000789b2",
      "name": "get_upload_operations",
      "credentials": {
        "postgres": {
          "name": "<your credential>"
        }
      }
    },
    {
      "parameters": {
        "jsCode": "const items = $input.all().map(i => i.json);\n\nconst groups = {};\nfor (const item of items) {\n  const key = item.recipe_ref;\n  if (!groups[key]) {\n    const [server, port] = item.account_id.split(',');\n    const [sampleType, processingSetting] = item.pipeline_id.split(',');\n    groups[key] = {\n      recipe_ref: item.recipe_ref,\n      server: server.trim(),\n      port: port.trim(),\n      sample_type: sampleType.trim(),\n      processing_setting: processingSetting.trim(),\n      operations: []\n    };\n  }\n  groups[key].operations.push({\n    operation_ref: item.operation_ref,\n    idat_ref: item.idat_ref\n  });\n}\n\nreturn Object.values(groups).map(g => ({ \n  json: {\n    ...g,\n    operations: JSON.stringify(g.operations)\n  } \n}));"
      },
      "type": "n8n-nodes-base.code",
      "typeVersion": 2,
      "position": [
        -16,
        -80
      ],
      "id": "3231deab-8dcc-49ea-93fb-705528a89fa8",
      "name": "group_by_recipe"
    },
    {
      "parameters": {
        "operation": "executeQuery",
        "query": "SELECT \n  i.uniqueref AS idat_ref,\n  i.sample_id,\n  i.position,\n  s.sentrix_id\nFROM idats i\nJOIN scans s ON s.uniqueref = i.scan_ref\nWHERE i.uniqueref IN (\n  SELECT (value->>'idat_ref')::bigint\n  FROM jsonb_array_elements(('{{ $json.operations }}'::text)::jsonb) AS value\n);",
        "options": {}
      },
      "type": "n8n-nodes-base.postgres",
      "typeVersion": 2.6,
      "position": [
        496,
        -64
      ],
      "id": "c5ff6bfc-e6ea-4acf-93f5-2ee9d7d30993",
      "name": "get_idats",
      "credentials": {
        "postgres": {
          "name": "<your credential>"
        }
      }
    },
    {
      "parameters": {
        "jsCode": "const idats = $input.all().map(i => i.json);\nconst loopItem = $('group_by_recipe').item.json;\n\nconst sampleType = loopItem.sample_type;\nconst processingSetting = loopItem.processing_setting;\n\nconst header = 'Sample Name\\tFilename\\tSample Type\\tProcessing Setting\\tDisplay Name';\n\nconst rows = idats.map(idat => {\n  const sampleName = `${idat.sentrix_id}_${idat.position}`;\n  const filename = `/volume1/ALLDATA/Scans/GTCs/${idat.sentrix_id}_${idat.position}.gtc`;\n  return `${sampleName}\\t${filename}\\t${sampleType}\\t${processingSetting}\\t${idat.sample_id}`;\n});\n\nconst batchContent = [header, ...rows].join('\\n');\n\nreturn [{\n  json: {\n    batch_content: batchContent,\n    server: loopItem.server,\n    port: loopItem.port,\n    recipe_ref: loopItem.recipe_ref,\n    operations: loopItem.operations\n  }\n}];"
      },
      "type": "n8n-nodes-base.code",
      "typeVersion": 2,
      "position": [
        704,
        -64
      ],
      "id": "f060e1bd-c41d-4cbe-b97f-e9d1437d1df9",
      "name": "build_batch_txt"
    },
    {
      "parameters": {
        "options": {}
      },
      "type": "n8n-nodes-base.splitInBatches",
      "typeVersion": 3,
      "position": [
        192,
        -80
      ],
      "id": "08ef0dfd-686c-4187-9111-b05766aa4307",
      "name": "Loop Over Items"
    },
    {
      "parameters": {
        "command": "=cat > /home/genera/nxclinical/batch.txt << 'BATCHEOF'\n{{ $json.batch_content }}\nBATCHEOF"
      },
      "type": "n8n-nodes-base.executeCommand",
      "typeVersion": 1,
      "position": [
        896,
        -64
      ],
      "id": "e9a1bf68-4cc8-4f20-bf87-318456295bb0",
      "name": "write_batch_file"
    },
    {
      "parameters": {
        "command": "=export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64 && export PATH=$JAVA_HOME/bin:$PATH && \"/home/genera/nxclinical/BioDiscovery/NxClinical Sample Importer/NxClinicalSampleImporter\" -server={{ $('build_batch_txt').item.json.server }} -port={{ $('build_batch_txt').item.json.port }} -user=gulsahsimsir -password=gulsah123 -descriptorFile=\"/home/genera/nxclinical/batch.txt\" -overrideExisting=true"
      },
      "type": "n8n-nodes-base.executeCommand",
      "typeVersion": 1,
      "position": [
        1088,
        -64
      ],
      "id": "1a98b8d0-4468-491c-9baa-2c5022131db4",
      "name": "run_nxclinical"
    },
    {
      "parameters": {
        "operation": "executeQuery",
        "query": "UPDATE data_operations_array\nSET status_concept_ref = 29,\n    performed_at = NOW(),\n    updated_at = NOW()\nWHERE uniqueref IN (\n  SELECT (value->>'operation_ref')::bigint\n  FROM jsonb_array_elements(('{{ $('build_batch_txt').item.json.operations }}'::text)::jsonb) AS value\n);",
        "options": {}
      },
      "type": "n8n-nodes-base.postgres",
      "typeVersion": 2.6,
      "position": [
        1280,
        -64
      ],
      "id": "c4bf8a00-dd2e-4d17-a9b6-a3911d246323",
      "name": "update_operations_completed",
      "credentials": {
        "postgres": {
          "name": "<your credential>"
        }
      }
    },
    {
      "parameters": {
        "command": "rm /home/genera/nxclinical/batch.txt"
      },
      "type": "n8n-nodes-base.executeCommand",
      "typeVersion": 1,
      "position": [
        1904,
        -64
      ],
      "id": "0cfcb9a8-4498-4fb5-8cbd-02b95f176e3e",
      "name": "delete_batch_file"
    },
    {
      "parameters": {
        "fromEmail": "bioinf.notify@gen-era.tech",
        "toEmail": "hande.beklen@gen-era.com.tr",
        "subject": "NxClinical Y\u00fckleme Bildirimi",
        "html": "={{ $json.email_body }}",
        "options": {}
      },
      "type": "n8n-nodes-base.emailSend",
      "typeVersion": 2.1,
      "position": [
        848,
        -352
      ],
      "id": "6dc27558-d57f-472d-a3f2-06f9e8e7a8ae",
      "name": "Send email",
      "credentials": {
        "smtp": {
          "name": "<your credential>"
        }
      }
    },
    {
      "parameters": {
        "operation": "executeQuery",
        "query": "SELECT DISTINCT\n  i.sample_id\nFROM data_operations_array doa\nJOIN idats i ON i.uniqueref = doa.idat_ref\nWHERE doa.status_concept_ref = 29\nAND doa.recipe_ref IN (457, 490)\nAND doa.performed_at >= NOW() - INTERVAL '1 hour';",
        "options": {}
      },
      "type": "n8n-nodes-base.postgres",
      "typeVersion": 2.6,
      "position": [
        448,
        -352
      ],
      "id": "794d4a1e-9453-4939-90eb-9014c4d4af06",
      "name": "get_completed_operations",
      "executeOnce": true,
      "credentials": {
        "postgres": {
          "name": "<your credential>"
        }
      }
    },
    {
      "parameters": {
        "jsCode": "const items = $input.all().map(i => i.json);\n\nconst sampleList = items.map(i => `<li>${i.sample_id}</li>`).join('\\n');\n\nconst body = `\n<p>A\u015fa\u011f\u0131daki \u00f6rnekler NxClinical platformuna y\u00fcklenmi\u015ftir.</p>\n<ul>\n${sampleList}\n</ul>\n`;\n\nreturn [{\n  json: {\n    email_body: body\n  }\n}];"
      },
      "type": "n8n-nodes-base.code",
      "typeVersion": 2,
      "position": [
        656,
        -352
      ],
      "id": "02081272-447d-4cec-b006-01082170b98a",
      "name": "build_email_content"
    },
    {
      "parameters": {
        "operation": "executeQuery",
        "query": "SELECT\n    p.id AS operator_email,\n    p.name AS operator_name,\n\n    doa.recipe_ref,\n\n    STRING_AGG(DISTINCT s.sentrix_id, ', ' ORDER BY s.sentrix_id) AS run_ids,\n    STRING_AGG(DISTINCT cs.care_site_name, ', ' ORDER BY cs.care_site_name) AS sample_owners,\n\n    STRING_AGG(DISTINCT dor.account_id, ', ' ORDER BY dor.account_id) AS account_id,\n\n    STRING_AGG(DISTINCT k.name, ', ' ORDER BY k.name) AS kit_names,\n\n    STRING_AGG(\n        DISTINCT COALESCE(\n            NULLIF(dor.pipeline_name, ''),\n            NULLIF(split_part(dor.pipeline_id, ',', 2), ''),\n            NULLIF(split_part(dor.pipeline_id, ',', 1), ''),\n            '-'\n        ),\n        ', '\n        ORDER BY COALESCE(\n            NULLIF(dor.pipeline_name, ''),\n            NULLIF(split_part(dor.pipeline_id, ',', 2), ''),\n            NULLIF(split_part(dor.pipeline_id, ',', 1), ''),\n            '-'\n        )\n    ) AS pipeline_name,\n\n    COUNT(DISTINCT doa.uniqueref) AS total_data_operations,\n    STRING_AGG(DISTINCT i.sample_id, ', ' ORDER BY i.sample_id) AS sample_ids\n\nFROM data_operations_array doa\n\nJOIN providers p\n    ON p.uniqueref = doa.operator_ref\n\nJOIN idats i\n    ON i.uniqueref = doa.idat_ref\n\nJOIN scans s\n    ON s.uniqueref = i.scan_ref\n\nJOIN data_operation_recipes dor\n    ON dor.uniqueref = doa.recipe_ref\n\nLEFT JOIN kits k\n    ON k.uniqueref = dor.kit_ref\n\nLEFT JOIN care_site cs\n    ON cs.uniqueref = i.requesting_caresite_ref\n\nWHERE doa.recipe_ref = {{ $('build_batch_txt').first().json.recipe_ref }}\n  AND doa.uniqueref IN (\n    {{ JSON.parse($('build_batch_txt').first().json.operations).map(o => o.operation_ref).join(',') }}\n  )\n  AND doa.status_concept_ref = 29\n  AND p.id IS NOT NULL\n\nGROUP BY\n    p.id,\n    p.name,\n    doa.recipe_ref;",
        "options": {}
      },
      "type": "n8n-nodes-base.postgres",
      "typeVersion": 2.6,
      "position": [
        1488,
        -64
      ],
      "id": "e3ae38c9-f305-445d-8006-f1beef719c69",
      "name": "get_operator_mail_and_upload_summary",
      "credentials": {
        "postgres": {
          "name": "<your credential>"
        }
      }
    },
    {
      "parameters": {
        "fromEmail": "bioinf.notify@gen-era.tech",
        "toEmail": "={{ $json.operator_email }}",
        "subject": "=NxClinical y\u00fcklemesi tamamland\u0131 - {{ $json.run_ids }}",
        "html": "=<!DOCTYPE html>\n<html lang=\"tr\">\n<head><meta charset=\"UTF-8\"><meta name=\"viewport\" content=\"width=device-width,initial-scale=1\"></head>\n<body style=\"margin:0;padding:0;background:#f4f6f8;font-family:-apple-system,BlinkMacSystemFont,'Segoe UI',Roboto,Helvetica,Arial,sans-serif;color:#1f2933;\">\n  <table role=\"presentation\" width=\"100%\" cellpadding=\"0\" cellspacing=\"0\" border=\"0\" style=\"background:#f4f6f8;padding:32px 16px;\">\n    <tr><td align=\"center\">\n      <table role=\"presentation\" width=\"600\" cellpadding=\"0\" cellspacing=\"0\" border=\"0\" style=\"max-width:600px;background:#ffffff;border-radius:12px;overflow:hidden;box-shadow:0 1px 3px rgba(0,0,0,0.06);\">\n\n        <tr>\n          <td style=\"padding:24px 32px 20px 32px;border-bottom:1px solid #e4e7eb;\">\n            <table role=\"presentation\" width=\"100%\" cellpadding=\"0\" cellspacing=\"0\" border=\"0\">\n              <tr>\n                <td style=\"vertical-align:middle;\">\n                  <img src=\"data:image/gif;base64,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\" alt=\"Era\" height=\"36\" style=\"display:block;border:0;outline:none;text-decoration:none;height:36px;\">\n                </td>\n                <td align=\"right\" style=\"vertical-align:middle;\">\n                  <img src=\"data:image/png;base64,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\" alt=\"Tamamland\u0131\" width=\"36\" height=\"36\" style=\"display:inline-block;border:0;outline:none;text-decoration:none;width:36px;height:36px;vertical-align:middle;\">\n                </td>\n              </tr>\n            </table>\n            <div style=\"font-size:20px;font-weight:600;margin-top:18px;line-height:1.3;color:#102a43;\">NxClinical Y\u00fcklemesi Tamamland\u0131</div>\n          </td>\n        </tr>\n\n        <tr>\n          <td style=\"padding:26px 32px 4px 32px;\">\n            <p style=\"margin:0 0 14px 0;font-size:15px;line-height:1.55;\">Merhaba {{ $json.operator_name }},</p>\n            <p style=\"margin:0 0 20px 0;font-size:15px;line-height:1.55;\">\n              Ba\u015flatm\u0131\u015f oldu\u011funuz NxClinical y\u00fcklemesi ba\u015far\u0131yla tamamland\u0131. Detaylar a\u015fa\u011f\u0131dad\u0131r.\n            </p>\n          </td>\n        </tr>\n\n        <tr>\n          <td style=\"padding:0 32px 4px 32px;\">\n            <table role=\"presentation\" width=\"100%\" cellpadding=\"0\" cellspacing=\"0\" border=\"0\" style=\"border:1px solid #e4e7eb;border-radius:8px;border-collapse:separate;border-spacing:0;\">\n              <tr>\n                <td style=\"padding:12px 16px;border-bottom:1px solid #e4e7eb;font-size:13px;color:#52606d;width:170px;\">Run ID</td>\n                <td style=\"padding:12px 16px;border-bottom:1px solid #e4e7eb;font-size:14px;font-family:'SFMono-Regular',Menlo,Consolas,monospace;color:#102a43;\">{{ $json.run_ids }}</td>\n              </tr>\n              <tr>\n                <td style=\"padding:12px 16px;border-bottom:1px solid #e4e7eb;font-size:13px;color:#52606d;\">Numune Sahibi</td>\n                <td style=\"padding:12px 16px;border-bottom:1px solid #e4e7eb;font-size:14px;font-family:'SFMono-Regular',Menlo,Consolas,monospace;color:#102a43;\">{{ $json.sample_owners }}</td>\n              </tr>\n              <tr>\n                <td style=\"padding:12px 16px;border-bottom:1px solid #e4e7eb;font-size:13px;color:#52606d;\">Hesap (Account ID)</td>\n                <td style=\"padding:12px 16px;border-bottom:1px solid #e4e7eb;font-size:14px;font-family:'SFMono-Regular',Menlo,Consolas,monospace;color:#102a43;\">{{ $json.account_id }}</td>\n              </tr>\n              <tr>\n                <td style=\"padding:12px 16px;border-bottom:1px solid #e4e7eb;font-size:13px;color:#52606d;\">Kit</td>\n                <td style=\"padding:12px 16px;border-bottom:1px solid #e4e7eb;font-size:14px;font-family:'SFMono-Regular',Menlo,Consolas,monospace;color:#102a43;\">{{ $json.kit_names }}</td>\n              </tr>\n              <tr>\n                <td style=\"padding:12px 16px;border-bottom:1px solid #e4e7eb;font-size:13px;color:#52606d;\">Pipeline</td>\n                <td style=\"padding:12px 16px;border-bottom:1px solid #e4e7eb;font-size:14px;font-family:'SFMono-Regular',Menlo,Consolas,monospace;color:#102a43;\">{{ $json.pipeline_name || '-' }}</td>\n              </tr>\n              <tr>\n                <td style=\"padding:12px 16px;font-size:13px;color:#52606d;\">Y\u00fcklenen \u00f6rnek say\u0131s\u0131</td>\n                <td style=\"padding:12px 16px;font-size:14px;font-family:'SFMono-Regular',Menlo,Consolas,monospace;color:#102a43;\"><strong>{{ $json.total_data_operations }}</strong></td>\n              </tr>\n            </table>\n          </td>\n        </tr>\n\n        <tr>\n          <td style=\"padding:24px 32px 4px 32px;\">\n            <div style=\"font-size:12px;color:#52606d;margin-bottom:10px;text-transform:uppercase;letter-spacing:0.7px;font-weight:600;\">Y\u00fcklenen \u00d6rnekler</div>\n            <table role=\"presentation\" width=\"100%\" cellpadding=\"0\" cellspacing=\"0\" border=\"0\" style=\"border:1px solid #e4e7eb;border-radius:8px;border-collapse:separate;border-spacing:0;background:#fafbfc;\">\n              {{ ($json.sample_ids || '').split(', ').filter(Boolean).map((s, i, arr) => `<tr><td style=\"padding:10px 16px;${i < arr.length - 1 ? 'border-bottom:1px solid #e4e7eb;' : ''}font-size:13px;color:#7b8794;width:36px;\">${String(i+1).padStart(2,'0')}</td><td style=\"padding:10px 16px;${i < arr.length - 1 ? 'border-bottom:1px solid #e4e7eb;' : ''}font-size:14px;font-family:'SFMono-Regular',Menlo,Consolas,monospace;color:#102a43;\">${s}</td></tr>`).join('') }}\n            </table>\n          </td>\n        </tr>\n\n        <tr>\n          <td style=\"padding:24px 32px 28px 32px;\">\n            <p style=\"margin:0;font-size:13px;color:#7b8794;line-height:1.55;\">\n              Bu, otomatik bir bildirimdir; l\u00fctfen bu e-postaya yan\u0131t vermeyiniz. Sorular\u0131n\u0131z i\u00e7in\n              <a href=\"mailto:can.holyavkin@gen-era.com.tr\" style=\"color:#0f766e;text-decoration:none;font-weight:500;\">hande.beklen@gen-era.com.tr</a>\n              adresine e-posta atabilirsiniz.\n            </p>\n          </td>\n        </tr>\n\n        <tr>\n          <td style=\"background:#f4f6f8;padding:14px 32px;text-align:center;font-size:11px;color:#9aa5b1;letter-spacing:0.4px;\">\n            Gen-Era Diagnostik \u00b7 Biyoinformatik \u00c7\u00f6z\u00fcmler\n          </td>\n        </tr>\n      </table>\n    </td></tr>\n  </table>\n</body>\n</html>",
        "options": {
          "appendAttribution": false
        }
      },
      "type": "n8n-nodes-base.emailSend",
      "typeVersion": 2.1,
      "position": [
        1696,
        -64
      ],
      "id": "abb3b239-a605-49b1-a513-c3a9becc6e84",
      "name": "Send upload completed email",
      "credentials": {
        "smtp": {
          "name": "<your credential>"
        }
      }
    }
  ],
  "connections": {
    "When clicking \u2018Execute workflow\u2019": {
      "main": [
        [
          {
            "node": "get_upload_operations",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "get_upload_operations": {
      "main": [
        [
          {
            "node": "group_by_recipe",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "group_by_recipe": {
      "main": [
        [
          {
            "node": "Loop Over Items",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "get_idats": {
      "main": [
        [
          {
            "node": "build_batch_txt",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "Loop Over Items": {
      "main": [
        [
          {
            "node": "get_completed_operations",
            "type": "main",
            "index": 0
          }
        ],
        [
          {
            "node": "get_idats",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "build_batch_txt": {
      "main": [
        [
          {
            "node": "write_batch_file",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "write_batch_file": {
      "main": [
        [
          {
            "node": "run_nxclinical",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "run_nxclinical": {
      "main": [
        [
          {
            "node": "update_operations_completed",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "update_operations_completed": {
      "main": [
        [
          {
            "node": "get_operator_mail_and_upload_summary",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "delete_batch_file": {
      "main": [
        [
          {
            "node": "Loop Over Items",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "get_completed_operations": {
      "main": [
        [
          {
            "node": "build_email_content",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "build_email_content": {
      "main": [
        [
          {
            "node": "Send email",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "get_operator_mail_and_upload_summary": {
      "main": [
        [
          {
            "node": "Send upload completed email",
            "type": "main",
            "index": 0
          }
        ]
      ]
    },
    "Send upload completed email": {
      "main": [
        [
          {
            "node": "delete_batch_file",
            "type": "main",
            "index": 0
          }
        ]
      ]
    }
  },
  "settings": {
    "executionOrder": "v1",
    "availableInMCP": false
  },
  "staticData": null,
  "meta": {
    "templateCredsSetupCompleted": true
  },
  "versionId": "9eb40ddc-1cf9-4927-beed-c913673d1aa0",
  "activeVersionId": null,
  "triggerCount": 0,
  "shared": [
    {
      "updatedAt": "2026-06-01T08:05:32.736Z",
      "createdAt": "2026-06-01T08:05:32.736Z",
      "role": "workflow:owner",
      "workflowId": "9z4hRpQRHcHn1c2K",
      "projectId": "wmZSbmn0RiQYcSpN"
    }
  ],
  "activeVersion": null,
  "tags": [],
  "commitDate": "12-07-2026/0:00",
  "fileName": "Nxclinical_uploder.json"
}

Credentials you'll need

Each integration node will prompt for credentials when you import. We strip credential IDs before publishing — you'll add your own.

• postgres
• smtp

About this workflow

Nxclinical_uploder. Uses executeWorkflowTrigger, executeCommand, postgres, emailSend. Event-driven trigger; 15 nodes.

Source: https://github.com/gen-era/N8N-backup/blob/45bc1509722def960f53853a786d0b1966d51ff6/Nxclinical_uploder.json — original creator credit. Request a take-down →

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