Olamide Isreal
9e6a16c19b
Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
326 lines
10 KiB
JSON
326 lines
10 KiB
JSON
{
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"params": {
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"// SYNTHEA PARAMETERS": {},
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"n_pat": {
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"type": "integer",
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"description": "Number of patients to generate (must be >= 2)",
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"default": 2,
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.n_pat",
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"examples": [2, 10, 100],
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"pattern": "^[0-9]+$",
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"validation": {
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"min": 2
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},
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"notes": "Minimum of 2 patients required (one male, one female)"
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},
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"percent_male": {
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"type": "number",
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"description": "Percentage of male patients (between 0-1)",
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"default": 0.5,
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.percent_male",
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"examples": [0.0, 0.5, 1.0],
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"pattern": "^0(\\.\\d+)?|1(\\.0)?$",
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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": "Value must be between 0 and 1 inclusive"
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},
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"imputed_store": {
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"type": "folder",
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"description": "Path to imputed UKBB data",
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"default": "/mnt/Avatar/imputed/ukbb/imputed",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.imputed_store",
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"examples": [
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"/mnt/Avatar/imputed/ukbb/imputed",
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"/rosalind/ukbb/imputed"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Directory containing imputed UKBB data"
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},
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"pheno_store": {
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"type": "file",
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"description": "Path to phenotype data file",
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"default": "/mnt/Avatar/dd/synthea/metadata/ukbb_phenotypes_filtered.csv",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.pheno_store",
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"examples": [
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"/mnt/Avatar/dd/synthea/metadata/ukbb_phenotypes_filtered.csv"
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],
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"pattern": ".*\\.csv$",
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"validation": {},
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"notes": "CSV file containing filtered UKBB phenotype data"
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},
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"disease": {
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"type": "string",
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"description": "Disease or condition to simulate",
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"default": "schizophrenia",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.disease",
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"examples": [
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"schizophrenia",
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"healthy",
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"leukaemia",
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"Purpura and other haemorrhagic conditions"
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],
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"pattern": ".*",
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"enum": [
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"schizophrenia",
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"healthy",
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"leukaemia",
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"Purpura and other haemorrhagic conditions"
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],
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"validation": {},
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"notes": "Use 'healthy' for healthy individuals or specify a disease condition"
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},
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"healthy_dir": {
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"type": "folder",
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"description": "Path to healthy patient data directory",
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"default": "/Workspace/next/registry/pipelines/digital_patient",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.healthy_dir",
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"examples": [
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"/Workspace/next/registry/pipelines/digital_patient",
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"/mnt/Avatar/digital_patient"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Directory containing data for healthy patient generation"
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},
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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/omic-next-apis/wes/digital_patients",
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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/dd/digital_patient",
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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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"// BORZOI PARAMETERS": {},
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"container_borzoi": {
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"type": "string",
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"description": "Borzoi container image",
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"default": "borzoi:latest",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.container_borzoi",
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"examples": [
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"borzoi:latest",
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"borzoi: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 Borzoi module"
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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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"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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"schizophrenia_study"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Identifier for the digital patient project"
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},
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"mane": {
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"type": "file",
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"description": "Path to MANE reference file",
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"default": "/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.mane",
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"examples": [
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"/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv"
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],
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"pattern": ".*\\.tsv$",
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"validation": {},
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"notes": "MANE transcripts reference file in TSV format"
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},
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"// VCF2PROT PARAMETERS": {},
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"container_vcf2prot": {
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"type": "string",
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"description": "VCF2PROT container image",
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"default": "vcf2prot:latest",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.container_vcf2prot",
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"examples": [
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"vcf2prot:latest",
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"vcf2prot: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 VCF2PROT module"
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},
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"// RNA2PROTEINEXPRESSION PARAMETERS": {},
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"container_rna2protexpression": {
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"type": "string",
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"description": "RNA2PROTEINEXPRESSION container image",
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"default": "rna2protexpression:latest",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.container_rna2protexpression",
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"examples": [
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"rna2protexpression:latest",
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"rna2protexpression: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 RNA2PROTEINEXPRESSION module"
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},
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"containerOptions_rna2protexpression": {
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"type": "string",
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"description": "Container options for RNA2PROTEINEXPRESSION",
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"default": "--gpus all --rm -v /mnt:/mnt -v /dbs:/dbs",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.containerOptions_rna2protexpression",
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"examples": [
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"--gpus all --rm -v /mnt:/mnt -v /dbs:/dbs"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Docker container runtime options for RNA2PROTEINEXPRESSION with GPU and database volume mounts"
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},
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"// CORTO PARAMETERS": {},
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"container_corto": {
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"type": "string",
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"description": "CORTO container image",
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"default": "corto:latest",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.container_corto",
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"examples": [
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"corto:latest",
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"corto: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 CORTO module"
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},
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"regulon": {
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"type": "file",
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"description": "Path to regulon RDA file",
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"default": "/Workspace/next/registry/pipelines/digital_patient/regulon.rda",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.regulon",
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"examples": [
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"/Workspace/next/registry/pipelines/digital_patient/regulon.rda"
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],
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"pattern": ".*\\.rda$",
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"validation": {},
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"notes": "Regulon data file in RDA format for CORTO module"
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},
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"// CIBERSORT PARAMETERS": {},
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"cibersortx_username": {
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"type": "string",
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"description": "CIBERSORTx username for authentication",
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"default": "gabriel.richman.2009@anderson.ucla.edu",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.cibersortx_username",
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"examples": [
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"gabriel.richman.2009@anderson.ucla.edu"
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],
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"pattern": "^[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\\.[a-zA-Z]{2,}$",
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"validation": {},
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"notes": "Username (email) for CIBERSORTx authentication"
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},
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"cibersortx_token": {
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"type": "string",
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"description": "CIBERSORTx authentication token",
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"default": "b5b39e563fb947df4cfd4843d40fdb99",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.cibersortx_token",
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"examples": [
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"b5b39e563fb947df4cfd4843d40fdb99"
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],
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"pattern": "^[a-f0-9]{32}$",
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"validation": {},
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"notes": "Authentication token for CIBERSORTx API access"
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},
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"container_ecotyper": {
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"type": "string",
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"description": "ECOTyper container image",
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"default": "ecotyper:latest",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.container_ecotyper",
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"examples": [
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"ecotyper:latest",
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"ecotyper: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 ECOTyper module"
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},
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"signature_matrix": {
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"type": "file",
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"description": "Path to signature matrix file",
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"default": "/Workspace/next/registry/pipelines/digital_patient/LM22_sourceGEP_ensg.txt",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.signature_matrix",
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"examples": [
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"/Workspace/next/registry/pipelines/digital_patient/LM22_sourceGEP_ensg.txt"
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],
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"pattern": ".*\\.txt$",
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"validation": {},
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"notes": "Signature matrix file for CIBERSORTx analysis"
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},
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"ecotyper_outdir": {
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"type": "folder",
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"description": "Output directory for ECOTyper results",
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"default": "/mnt/omic-next-apis/wes/digital-patients/ecotyper",
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"required": true,
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"pipeline_io": "output",
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"var_name": "params.ecotyper_outdir",
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"examples": [
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"/mnt/OmicNAS/olamide/ecotyper/results/ecotyper"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Directory where ECOTyper results will be stored"
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}
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}
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}
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