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
71 lines
2.0 KiB
Plaintext
71 lines
2.0 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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// Default parameters
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params.disease_name = null
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params.outdir = null
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params.population = 10
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params.gender = 0.5
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params.min_age = 0
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params.max_age = 90
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params.seed = null
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// Validate required parameters
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if (!params.disease_name) {
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error "Disease name is required. Please specify with --disease_name"
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}
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if (!params.outdir) {
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error "Output directory is required. Please specify with --outdir"
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}
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// Process to generate synthetic patients
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process generatePatients {
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container 'harbor.cluster.omic.ai/omic/synthea-alldiseases:latest'
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publishDir params.outdir, mode: 'copy'
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input:
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val diseaseName
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output:
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path "fhir/*.json", optional: true, emit: fhir_output
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path "run.log", emit: log_file
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script:
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def moduleBasename = diseaseName.toLowerCase().replaceAll(' ', '_')
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def genderArg = params.gender < 0.5 ? "M" : (params.gender > 0.5 ? "F" : "B")
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def seedArg = params.seed ? "-s ${params.seed}" : ""
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"""
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# Check if a custom module exists, otherwise use built-in Synthea modules
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MODULE_FILE="/app/src/main/resources/modules/${moduleBasename}.json"
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if [ -f "\${MODULE_FILE}" ]; then
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echo "Found custom module: \${MODULE_FILE}" | tee run.log
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else
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echo "Using built-in Synthea modules for: ${diseaseName}" | tee run.log
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fi
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# Run Synthea patient generation
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cd /app && ./run_synthea \
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-p ${params.population} \
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-g ${genderArg} \
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-a ${params.min_age}-${params.max_age} \
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${seedArg} \
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-- ${diseaseName} 2>&1 | tee -a run.log
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# Collect FHIR output
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mkdir -p fhir
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if [ -d /app/output/fhir ]; then
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cp /app/output/fhir/*.json fhir/ 2>/dev/null || true
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echo "Copied \$(ls fhir/*.json 2>/dev/null | wc -l) FHIR bundles" | tee -a run.log
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else
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echo "Warning: No FHIR output generated" | tee -a run.log
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fi
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"""
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}
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// Workflow
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workflow {
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generatePatients(params.disease_name)
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}
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