Digital Trials pipeline configured for WES
Source-only snapshot of the cluster branch for WES execution. Large reference files (HPA/MANE/ensemble FASTA, model weights, ~597 MB) are omitted: they are baked into the container images at build time and mounted from the dreamdock-data PVC at runtime, and exceed the Gitea request size limit. Pipeline entry point is main.nf, which orchestrates the biotransformer, conplex and tissue modules as a single workflow. Ligand inputs are read from the eureka workspace; protein_zarr and chembl_db come from the dreamdock-data PVC.
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Olamide Isreal
192
params.json
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192
params.json
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{
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"params": {
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"// GENERAL PARAMETERS": {},
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"outdir": {
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"type": "folder",
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"description": "Output directory for results",
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"default": "/mnt/OmicNAS/private/old/gabe/digital_trials",
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"required": true,
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"pipeline_io": "output",
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"var_name": "params.outdir",
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"examples": [
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"/mnt/OmicNAS/private/old/gabe/digital_trials",
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"/path/to/custom/output"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Directory where all pipeline results will be stored"
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},
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"project_name": {
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"type": "string",
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"description": "Project identifier",
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"default": "test",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.project_name",
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"examples": [
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"test",
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"production",
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"drug_metabolism_study"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Identifier for the digital trials project"
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},
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"containerOptions": {
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"type": "string",
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"description": "Container runtime options",
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"default": "--gpus all --rm -v /mnt:/mnt",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.containerOptions",
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"examples": [
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"--gpus all --rm -v /mnt:/mnt",
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"--rm -v /data:/data"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Docker container runtime options for GPU usage and volume mounts"
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},
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"// BIOTRANSFORMER PARAMETERS": {},
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"container_biotransformer": {
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"type": "string",
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"description": "BioTransformer container image",
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"default": "biotransformer:latest",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.container_biotransformer",
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"examples": [
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"biotransformer:latest",
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"biotransformer:v1.0"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Docker container image for BioTransformer module"
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},
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"ligands": {
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"type": "folder",
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"description": "Path to input ligands directory",
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"default": "/Workspace/next/registry/pipelines/digital_trials/input",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.ligands",
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"examples": [
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"/Workspace/next/registry/pipelines/digital_trials/input",
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"/path/to/ligands"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Directory containing CSV files with ligand data for metabolic transformation"
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},
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"mode": {
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"type": "string",
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"description": "BioTransformer operation mode",
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"default": "HUMAN",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.mode",
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"examples": [
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"HUMAN",
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"SUPER",
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"MASS",
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"ORDERED"
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],
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"pattern": "^(HUMAN|SUPER|MASS|ORDERED)$",
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"enum": [
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"HUMAN",
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"SUPER",
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"MASS",
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"ORDERED"
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],
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"validation": {},
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"notes": "IMPORTANT: Use HUMAN mode as it's the only fully implemented option that returns expected metabolism to the last step"
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},
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"// CONPLEX PARAMETERS": {},
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"container_conplex": {
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"type": "string",
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"description": "CONPLEX container image",
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"default": "conplex_dig_pat:latest",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.container_conplex",
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"examples": [
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"conplex_dig_pat:latest",
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"conplex_dig_pat:v1.0"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Docker container image for CONPLEX module"
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},
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"mutated_protein_fasta": {
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"type": "folder",
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"description": "Path to mutated protein FASTA files directory",
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"default": "/Workspace/next/registry/pipelines/digital_trials/input",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.mutated_protein_fasta",
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"examples": [
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"/Workspace/next/registry/pipelines/digital_trials/input",
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"/path/to/protein/fasta/files"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Directory containing FASTA files with mutated protein sequences"
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},
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"threshold": {
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"type": "number",
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"description": "Binding affinity threshold for interactions",
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"default": 0.7,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.threshold",
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"examples": [
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0.5,
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0.7,
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0.9
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],
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"pattern": "^\\d+(\\.\\d+)?$",
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"validation": {
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"min": 0.0,
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"max": 1.0
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},
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"notes": "Threshold value for determining significant binding interactions"
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},
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"screening_batch_size": {
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"type": "integer",
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"description": "Batch size for virtual screening",
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"default": 100000,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.screening_batch_size",
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"examples": [
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10000,
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100000,
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1000000
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],
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"pattern": "^\\d+$",
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"validation": {
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"min": 1
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},
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"notes": "Batch size for virtual screening (100k is ideal to optimize performance)"
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},
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"protein_network_threshold": {
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"type": "number",
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"description": "Threshold for protein network analysis",
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"default": 0.95,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.protein_network_threshold",
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"examples": [
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0.9,
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0.95,
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0.99
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],
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"pattern": "^\\d+(\\.\\d+)?$",
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"validation": {
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"min": 0.0,
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"max": 1.0
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},
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"notes": "Threshold value for protein-protein interaction network construction"
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}
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}
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}
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