This workflow follows the Emailsend → Postgres recipe pattern — see all workflows that pair these two integrations.
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": "2026-06-11T06:30:21.216Z",
"createdAt": "2026-06-01T08:05:32.731Z",
"id": "9z4hRpQRHcHn1c2K",
"name": "Nxclinical_uploder",
"active": false,
"isArchived": false,
"nodes": [
{
"parameters": {
"workflowInputs": {
"values": [
{
"name": "path"
},
{
"name": "server"
},
{
"name": "port"
},
{
"name": "user"
},
{
"name": "password"
},
{
"name": "overrideExisting",
"type": "boolean"
}
]
}
},
"type": "n8n-nodes-base.executeWorkflowTrigger",
"typeVersion": 1.1,
"position": [
-448,
-320
],
"id": "e6e7738e-f17c-48f0-b0a2-6c62ef0f06cb",
"name": "When Executed by Another Workflow"
},
{
"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={{ $json.server }} -port={{ $json.port }} -user={{ $json.user }} -password={{ $json.password }} -descriptorFile=\"{{ $json.path }}\" -overrideExisting={{ $json.overrideExisting }}"
},
"type": "n8n-nodes-base.executeCommand",
"typeVersion": 1,
"position": [
-240,
-320
],
"id": "4a40fe2d-1b17-49aa-837f-fbd6a451f2dd",
"name": "Execute Command"
},
{
"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=false"
},
"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": [
1488,
-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"
}
],
"connections": {
"When Executed by Another Workflow": {
"main": [
[]
]
},
"Execute Command": {
"main": [
[]
]
},
"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": "delete_batch_file",
"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
}
]
]
}
},
"settings": {
"executionOrder": "v1",
"availableInMCP": false
},
"staticData": null,
"meta": {
"templateCredsSetupCompleted": true
},
"versionId": "d1794cf1-a5fa-4e45-983a-6e52f967627b",
"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": "14-06-2026/0:00",
"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.
postgressmtp
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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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