diff --git a/main.nf b/main.nf index c293112..696efae 100644 --- a/main.nf +++ b/main.nf @@ -22,7 +22,7 @@ if (!params.outdir) { // Process to generate synthetic patients process generatePatients { - container 'harbor.cluster.omic.ai/omic/synthea-alldiseases:v2' + container 'harbor.cluster.omic.ai/omic/synthea-alldiseases:v3' publishDir params.outdir, mode: 'copy' input: @@ -34,13 +34,13 @@ process generatePatients { script: def moduleBasename = diseaseName.toLowerCase().replaceAll(' ', '_') - def genderArg = params.gender < 0.5 ? "M" : (params.gender > 0.5 ? "F" : "B") + def genderArg = params.gender < 0.5 ? "-g M" : (params.gender > 0.5 ? "-g F" : "") def seedArg = params.seed ? "-s ${params.seed}" : "" """ # Use pre-built jar directly (bypasses Gradle which needs write access to .gradle) cd /app && java -jar /app/build/libs/synthea-with-dependencies.jar \ -p ${params.population} \ - -g ${genderArg} \ + ${genderArg} \ -a ${params.min_age}-${params.max_age} \ ${seedArg} 2>&1 | tee run.log diff --git a/nextflow.config b/nextflow.config index ab5b9b8..bf4e64c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -26,7 +26,7 @@ profiles { k8s { process { executor = 'k8s' - container = 'harbor.cluster.omic.ai/omic/synthea-alldiseases:v2' + container = 'harbor.cluster.omic.ai/omic/synthea-alldiseases:v3' } docker { enabled = true