Olamide Isreal
d468509ec3
- Rewrite params.json to match WES tool registry format - Update main.nf to use Harbor container image - Add k8s profile to nextflow.config for WES/Kubernetes execution - Use s3://omic/eureka paths for output
118 lines
3.6 KiB
JSON
118 lines
3.6 KiB
JSON
{
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"params": {
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"disease_name": {
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"type": "string",
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"description": "Disease name to generate synthetic patients for",
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"default": "Diabetes",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.disease_name",
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"examples": [
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"Diabetes",
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"Hypertension",
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"Lung Cancer"
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],
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"pattern": ".*",
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"enum": [],
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"validation": {},
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"notes": "The disease name used to find or generate a Synthea disease module. Case-insensitive."
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},
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"population": {
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"type": "integer",
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"description": "Number of synthetic patients to generate",
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"default": 10,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.population",
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"examples": [
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10,
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100,
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1000
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],
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"pattern": "^\\d+$",
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"enum": [],
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"validation": {
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"min": 1,
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"max": 10000
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},
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"notes": "Higher numbers take longer to generate."
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},
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"gender": {
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"type": "number",
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"description": "Proportion of female patients (0.0 = all male, 1.0 = all female)",
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"default": 0.5,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.gender",
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"examples": [
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0.5,
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0.0,
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1.0
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],
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"pattern": "^[01]\\.?\\d*$",
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"enum": [],
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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": "Decimal between 0.0 and 1.0 representing the proportion of female patients."
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},
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"min_age": {
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"type": "integer",
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"description": "Minimum age of generated patients",
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"default": 0,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.min_age",
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"examples": [
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0,
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18,
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40
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],
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"pattern": "^\\d+$",
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"enum": [],
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"validation": {
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"min": 0,
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"max": 140
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},
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"notes": "Minimum patient age in years."
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},
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"max_age": {
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"type": "integer",
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"description": "Maximum age of generated patients",
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"default": 90,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.max_age",
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"examples": [
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90,
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65,
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100
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],
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"pattern": "^\\d+$",
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"enum": [],
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"validation": {
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"min": 1,
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"max": 140
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},
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"notes": "Maximum patient age in years."
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},
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"outdir": {
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"type": "folder",
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"description": "Output directory for generated patient data",
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"default": "s3://omic/eureka/synthea-alldiseases/output",
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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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"s3://omic/eureka/synthea-alldiseases/output",
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"s3://omic/eureka/synthea-alldiseases/results"
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],
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"pattern": ".*",
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"enum": [],
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"validation": {},
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"notes": "Directory where generated FHIR patient bundles will be stored."
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}
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}
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}
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