Olamide Isreal
f8df39d9af
- Save pwd before cd /app so outputs go to correct location - Use set +e and PIPESTATUS to handle java exit code gracefully - Exit 0 if FHIR files were generated successfully
76 lines
2.0 KiB
Plaintext
76 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: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 moduleBasename = diseaseName.toLowerCase().replaceAll(' ', '_')
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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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# Use pre-built jar directly (bypasses Gradle which needs write access to .gradle)
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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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# Collect FHIR output back into Nextflow work dir
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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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FHIR_COUNT=\$(ls fhir/*.json 2>/dev/null | wc -l)
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echo "Copied \${FHIR_COUNT} FHIR bundles" | tee -a run.log
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else
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echo "Warning: No FHIR output directory found" | tee -a run.log
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fi
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# Exit 0 if we got FHIR output, regardless of java exit code
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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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workflow {
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generatePatients(params.disease_name)
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}
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