Olamide Isreal
67bd6692b0
- Remove unused variable and redundant comments/echo statements in main.nf - Remove obsolete files: simple.nf, test.nf, generate_patients.sh, test_synthea.sh, trace.txt, docker-compose.yml (all referenced local-only synthea-module-generator image)
66 lines
1.5 KiB
Plaintext
66 lines
1.5 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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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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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 generatePatients {
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container 'harbor.cluster.omic.ai/omic/synthea-alldiseases:v3'
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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 genderArg = params.gender < 0.5 ? "-g M" : (params.gender > 0.5 ? "-g F" : "")
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def seedArg = params.seed ? "-s ${params.seed}" : ""
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"""
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set +e
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WORKDIR=\$(pwd)
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# Run Synthea via pre-built jar (Gradle is not writable in K8s)
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cd /app
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java -jar /app/build/libs/synthea-with-dependencies.jar \
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-p ${params.population} \
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${genderArg} \
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-a ${params.min_age}-${params.max_age} \
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${seedArg} 2>&1 | tee \${WORKDIR}/run.log
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JAVA_EXIT=\${PIPESTATUS[0]}
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cd \${WORKDIR}
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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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fi
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# Succeed if FHIR output was produced
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if [ -n "\$(ls fhir/*.json 2>/dev/null)" ]; then
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exit 0
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else
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exit \${JAVA_EXIT}
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fi
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"""
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}
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workflow {
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generatePatients(params.disease_name)
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}
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