@seqera/node-red-seqera/examples/04 - RNA-seq to DifferentialAbundance.json

Node-RED nodes for interacting with the Seqera Platform API

[
  {
    "id": "a8f9e2c3d1b45678",
    "type": "tab",
    "label": "RNA-seq to DifferentialAbundance",
    "disabled": false,
    "info": "# RNA-seq to Differential Abundance Pipeline\n\nThis workflow demonstrates a complete RNA-seq analysis pipeline that:\n\n1. Takes user inputs (CSV samplesheet, base path, contrasts)\n2. Launches nf-core/rnaseq with dynamic output directory\n3. Monitors the rnaseq pipeline until completion\n4. On success, automatically launches nf-core/differentialabundance\n5. Uses outputs from rnaseq as inputs to differentialabundance\n6. Monitors differentialabundance until completion\n\n## Setup Requirements\n\n### Seqera Configuration\n- All Seqera nodes need a Seqera configuration to be assigned\n- Ensure your token has Launch permissions\n\n### Launchpad Pipelines\n- Create a Launchpad entry for nf-core/rnaseq\n- Create a Launchpad entry for nf-core/differentialabundance\n- Both should be pre-configured with compute environments and basic settings\n\n### Input Files\nYou'll need to prepare:\n1. **RNA-seq samplesheet CSV** - see example in documentation\n2. **Contrasts CSV** - defines comparisons for differential analysis\n3. **GTF annotation file** - path to reference annotation\n4. **Base output path** - e.g., s3://my-bucket/results or /path/to/results\n\n## How It Works\n\n1. Click the inject node and configure the inputs in the \"Set user inputs\" node\n2. The \"Generate outdir\" function creates a unique output directory from CSV basename\n3. nf-core/rnaseq launches with the samplesheet and generated outdir\n4. Monitor node polls status every 15 seconds\n5. On success, \"Prepare differentialabundance\" constructs file paths from rnaseq outputs\n6. nf-core/differentialabundance launches with the prepared parameters\n7. Monitor node tracks completion\n8. Debug nodes show status at each stage",
    "env": []
  },
  {
    "id": "inject_trigger",
    "type": "inject",
    "z": "a8f9e2c3d1b45678",
    "name": "Start Pipeline",
    "props": [],
    "repeat": "",
    "crontab": "",
    "once": false,
    "onceDelay": 0.1,
    "topic": "",
    "x": 120,
    "y": 200,
    "wires": [["set_user_inputs"]]
  },
  {
    "id": "set_user_inputs",
    "type": "function",
    "z": "a8f9e2c3d1b45678",
    "name": "Set user inputs",
    "func": "// USER CONFIGURATION - Edit these values\n// This example uses nf-core test data that works out of the box\n\n// Path to RNA-seq samplesheet CSV\n// Using small test dataset from this repository\nmsg.rnaseqSamplesheet = \"https://raw.githubusercontent.com/seqeralabs/node-red-seqera/main/docs/examples/data/rnaseq-tests-datasets.csv\";\n\n// Base output path (will be combined with CSV basename)\n// IMPORTANT: Change this to your actual output location\nmsg.basePath = \"s3://PATH_TO_YOUR_BUCKET\";\n\n// Path to contrasts CSV for differential abundance\n// This defines comparisons: WT vs RAP1_UNINDUCED, WT vs RAP1_IAA_30M, etc.\nmsg.contrastsCSV = \"https://raw.githubusercontent.com/seqeralabs/node-red-seqera/main/docs/examples/data/rnaseq-test-contrasts.csv\";\n\n// Genome parameter (use iGenomes reference)\n// The test data is S. cerevisiae (yeast)\nmsg.genome = \"R64-1-1\";\n\n// Launchpad pipeline names (must exist in your workspace)\nmsg.rnaseqLaunchpad = \"nf-core-rnaseq\";\nmsg.diffabundLaunchpad = \"nf-core-differentialabundance\";\n\n// Additional RNA-seq parameters (optional)\nmsg.rnaseqExtraParams = {\n    \"aligner\": \"star_salmon\",\n    \"pseudo_aligner\": null\n};\n\n// Store CSV path for later\nmsg.csvPath = msg.rnaseqSamplesheet;\n\nreturn msg;",
    "outputs": 1,
    "timeout": 0,
    "noerr": 0,
    "initialize": "",
    "finalize": "",
    "libs": [],
    "x": 300,
    "y": 200,
    "wires": [["generate_outdir"]]
  },
  {
    "id": "generate_outdir",
    "type": "function",
    "z": "a8f9e2c3d1b45678",
    "name": "Generate outdir",
    "func": "// Extract basename from CSV path\nconst csvPath = msg.rnaseqSamplesheet;\nconst pathParts = csvPath.split('/');\nconst csvFilename = pathParts[pathParts.length - 1];\nconst csvBasename = csvFilename.replace(/\\.csv$/i, '');\n\n// Remove trailing slash from base path if present\nconst basePath = msg.basePath.replace(/\\/$/, '');\n\n// Construct output directory\nmsg.outdir = `${basePath}/${csvBasename}`;\n\n// Store for later use\nmsg.rnaseqOutdir = msg.outdir;\n\nnode.status({fill: \"blue\", shape: \"dot\", text: `outdir: ${msg.outdir}`});\n\nreturn msg;",
    "outputs": 1,
    "timeout": 0,
    "noerr": 0,
    "initialize": "",
    "finalize": "",
    "libs": [],
    "x": 480,
    "y": 200,
    "wires": [["launch_rnaseq"]]
  },
  {
    "id": "launch_rnaseq",
    "type": "seqera-workflow-launch",
    "z": "a8f9e2c3d1b45678",
    "name": "Launch nf-core/rnaseq",
    "seqera": "37a74dee5cfd3aa6",
    "launchpadName": "rnaseqLaunchpad",
    "launchpadNameType": "msg",
    "paramsKey": "{\t   \"input\": msg.rnaseqSamplesheet,\t   \"outdir\": msg.outdir,\t   \"genome\": msg.genome,\t   \"aligner\": msg.rnaseqExtraParams.aligner\t}",
    "paramsKeyType": "jsonata",
    "workspaceId": "",
    "workspaceIdType": "str",
    "sourceWorkspaceId": "",
    "sourceWorkspaceIdType": "str",
    "x": 700,
    "y": 200,
    "wires": [["monitor_rnaseq"]]
  },
  {
    "id": "monitor_rnaseq",
    "type": "seqera-workflow-monitor",
    "z": "a8f9e2c3d1b45678",
    "name": "Monitor nf-core/rnaseq",
    "seqera": "37a74dee5cfd3aa6",
    "workflowId": "workflowId",
    "workflowIdType": "msg",
    "workspaceId": "",
    "workspaceIdType": "str",
    "keepPolling": true,
    "poll": "15",
    "pollUnits": "seconds",
    "x": 950,
    "y": 200,
    "wires": [["debug_rnaseq_running"], ["prepare_diffabund"], ["debug_rnaseq_failed"]]
  },
  {
    "id": "prepare_diffabund",
    "type": "function",
    "z": "a8f9e2c3d1b45678",
    "name": "Prepare differentialabundance inputs",
    "func": "// Extract the outdir that was used for rnaseq\nconst rnaseqOutdir = msg.rnaseqOutdir;\n\n// Remove trailing slash if present\nconst baseOutdir = rnaseqOutdir.replace(/\\/$/, '');\n\n// Construct paths to rnaseq outputs based on standard nf-core/rnaseq structure\n// Assumes STAR+Salmon quantification (most common)\nconst matrixPath = `${baseOutdir}/star_salmon/salmon.merged.gene_counts.tsv`;\nconst lengthMatrixPath = `${baseOutdir}/star_salmon/salmon.merged.gene_lengths.tsv`;\n\n// Prepare parameters for differentialabundance\n// The samplesheet needs to have a 'group' column (which becomes 'condition' for differential analysis)\nmsg.diffabundParams = {\n    \"input\": msg.rnaseqSamplesheet,  // Reuse the same samplesheet (must have 'group' column)\n    \"contrasts\": msg.contrastsCSV,\n    \"matrix\": matrixPath,\n    \"transcript_length_matrix\": lengthMatrixPath,\n    \"genome\": msg.genome,  // Use same genome as rnaseq\n    \"study_name\": msg.rnaseqOutdir.split('/').pop(),  // Use the basename as study name\n    \"study_type\": \"rnaseq\",\n    \"deseq2_vst_nsub\": 100, // Required to make test data work. Please set to a realistic value for real data!\n    \"outdir\": `${baseOutdir}_differentialabundance`\n};\n\nnode.status({\n    fill: \"green\", \n    shape: \"dot\", \n    text: \"RNA-seq complete, launching diffabund\"\n});\n\nreturn msg;",
    "outputs": 1,
    "timeout": 0,
    "noerr": 0,
    "initialize": "",
    "finalize": "",
    "libs": [],
    "x": 210,
    "y": 320,
    "wires": [["launch_diffabund"]]
  },
  {
    "id": "launch_diffabund",
    "type": "seqera-workflow-launch",
    "z": "a8f9e2c3d1b45678",
    "name": "Launch nf-core/differentialabundance",
    "seqera": "37a74dee5cfd3aa6",
    "launchpadName": "diffabundLaunchpad",
    "launchpadNameType": "msg",
    "paramsKey": "diffabundParams",
    "paramsKeyType": "msg",
    "workspaceId": "",
    "workspaceIdType": "str",
    "sourceWorkspaceId": "",
    "sourceWorkspaceIdType": "str",
    "x": 570,
    "y": 320,
    "wires": [["monitor_diffabund"]]
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    "id": "monitor_diffabund",
    "type": "seqera-workflow-monitor",
    "z": "a8f9e2c3d1b45678",
    "name": "Monitor nf-core/differentialabundance",
    "seqera": "37a74dee5cfd3aa6",
    "workflowId": "workflowId",
    "workflowIdType": "msg",
    "workspaceId": "",
    "workspaceIdType": "str",
    "keepPolling": true,
    "poll": "15",
    "pollUnits": "seconds",
    "x": 930,
    "y": 320,
    "wires": [["debug_diffabund_running"], ["debug_diffabund_success"], ["debug_diffabund_failed"]]
  },
  {
    "id": "debug_diffabund_running",
    "type": "debug",
    "z": "a8f9e2c3d1b45678",
    "name": "DiffAbund Running",
    "active": true,
    "tosidebar": true,
    "console": false,
    "tostatus": false,
    "complete": "payload.workflow.status",
    "targetType": "msg",
    "statusVal": "",
    "statusType": "auto",
    "x": 1230,
    "y": 280,
    "wires": []
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    "id": "debug_diffabund_success",
    "type": "debug",
    "z": "a8f9e2c3d1b45678",
    "name": "DiffAbund Complete",
    "active": true,
    "tosidebar": true,
    "console": false,
    "tostatus": false,
    "complete": "payload",
    "targetType": "msg",
    "statusVal": "",
    "statusType": "auto",
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    "wires": []
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    "id": "debug_diffabund_failed",
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    "active": true,
    "tosidebar": true,
    "console": false,
    "tostatus": false,
    "complete": "payload",
    "targetType": "msg",
    "statusVal": "",
    "statusType": "auto",
    "x": 1230,
    "y": 360,
    "wires": []
  },
  {
    "id": "comment_trigger",
    "type": "comment",
    "z": "a8f9e2c3d1b45678",
    "name": "1. Start: Configure inputs",
    "info": "Click the inject node to start the workflow.\n\nBefore running, open the \"Set user inputs\" function node\nand configure:\n- rnaseqSamplesheet: Path to your CSV file\n- basePath: Base output directory\n- contrastsCSV: Path to contrasts definition\n- gtfFile: Path to GTF annotation\n- rnaseqLaunchpad: Name of your rnaseq pipeline in Seqera\n- diffabundLaunchpad: Name of your differentialabundance pipeline",
    "x": 140,
    "y": 140,
    "wires": []
  },
  {
    "id": "comment_generate",
    "type": "comment",
    "z": "a8f9e2c3d1b45678",
    "name": "2. Generate unique output directory",
    "info": "This function extracts the CSV filename and creates\na unique output directory by combining:\n\nbasePath + CSV basename (without .csv extension)\n\nExample:\n- Input CSV: s3://bucket/data/experiment123.csv\n- Base path: s3://bucket/results\n- Output dir: s3://bucket/results/experiment123",
    "x": 540,
    "y": 140,
    "wires": []
  },
  {
    "id": "comment_rnaseq",
    "type": "comment",
    "z": "a8f9e2c3d1b45678",
    "name": "3. Launch & Monitor RNA-seq",
    "info": "Launches nf-core/rnaseq using the Launchpad configuration.\n\nParameters passed:\n- input: samplesheet CSV path\n- outdir: generated output directory\n- gtf: annotation file path\n- aligner: STAR+Salmon (default)\n\nThe monitor node polls every 15 seconds and has three outputs:\n- Port 1: Running status (continuous updates)\n- Port 2: Success (triggers next stage)\n- Port 3: Failed (goes to debug)",
    "x": 940,
    "y": 140,
    "wires": []
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  {
    "id": "comment_prepare",
    "type": "comment",
    "z": "a8f9e2c3d1b45678",
    "name": "4. Prepare DifferentialAbundance",
    "info": "Once RNA-seq succeeds, this function constructs the input\nparameters for nf-core/differentialabundance.\n\nIt builds file paths based on the known output structure:\n- matrix: star_salmon/salmon.merged.gene_counts.tsv\n- transcript_length_matrix: star_salmon/salmon.merged.gene_lengths.tsv\n\nReuses:\n- Same samplesheet (must include 'condition' column)\n- Same GTF file\n- Contrasts CSV for comparison definitions",
    "x": 370,
    "y": 380,
    "wires": []
  },
  {
    "id": "comment_diffabund",
    "type": "comment",
    "z": "a8f9e2c3d1b45678",
    "name": "5. Launch & Monitor DifferentialAbundance",
    "info": "Launches nf-core/differentialabundance with:\n- input: samplesheet with condition column\n- contrasts: comparison definitions\n- matrix: count matrix from RNA-seq\n- transcript_length_matrix: gene lengths from RNA-seq\n- gtf: same annotation used for RNA-seq\n- outdir: rnaseq_outdir + '_differentialabundance' suffix\n\nThe monitor node tracks completion and outputs to debug nodes.",
    "x": 900,
    "y": 380,
    "wires": []
  },
  {
    "id": "debug_rnaseq_failed",
    "type": "debug",
    "z": "a8f9e2c3d1b45678",
    "name": "RNA-seq Failed",
    "active": true,
    "tosidebar": true,
    "console": false,
    "tostatus": false,
    "complete": "payload",
    "targetType": "msg",
    "statusVal": "",
    "statusType": "auto",
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  {
    "id": "debug_rnaseq_running",
    "type": "debug",
    "z": "a8f9e2c3d1b45678",
    "name": "RNA-seq Running",
    "active": true,
    "tosidebar": true,
    "console": false,
    "tostatus": false,
    "complete": "payload.workflow.status",
    "targetType": "msg",
    "statusVal": "",
    "statusType": "auto",
    "x": 1230,
    "y": 180,
    "wires": []
  },
  {
    "id": "37a74dee5cfd3aa6",
    "type": "seqera-config",
    "baseUrl": "https://api.cloud.seqera.io",
    "workspaceId": "162690105070735"
  },
  {
    "id": "fb143a03b9f7e8af",
    "type": "global-config",
    "env": [],
    "modules": {
      "@seqera/node-red-seqera": "1.0.1"
    }
  }
]