tie java heap to task memory

EBIvariation · May 9, 2024 · c352362 · c352362
1 parent 4e1575c
commit c352362
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/eva_submission/nextflow/accession_and_load.nf b/eva_submission/nextflow/accession_and_load.nf
@@ -238,7 +238,7 @@ process accession_vcf {
 
 
     """
-    (java -Xmx6g -jar $params.jar.accession_pipeline --spring.config.location=file:$params.accession_job_props $pipeline_parameters) || \
+    (java -Xmx${task.memory.toGiga()}G -jar $params.jar.accession_pipeline --spring.config.location=file:$params.accession_job_props $pipeline_parameters) || \
     # If accessioning fails due to missing variants, but the only missing variants are structural variants,
     # then we should treat this as a success from the perspective of the automation.
     # TODO revert once accessioning pipeline properly registers structural variants
@@ -344,7 +344,7 @@ process load_variants_vcf {
     pipeline_parameters += " --spring.data.mongodb.database=" + db_name.toString()
 
     """
-    java -Xmx4G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.load_job_props --parameters.path=$params.load_job_props $pipeline_parameters
+    java -Xmx${task.memory.toGiga()}G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.load_job_props --parameters.path=$params.load_job_props $pipeline_parameters
     """
 }
 
@@ -386,7 +386,7 @@ process run_vep_on_variants {
     pipeline_parameters += " --app.vep.cache.species=" + vep_species.toString()
 
     """
-    java -Xmx4G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.load_job_props --parameters.path=$params.load_job_props $pipeline_parameters
+    java -Xmx${task.memory.toGiga()}G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.load_job_props --parameters.path=$params.load_job_props $pipeline_parameters
     """
 }
 
@@ -426,7 +426,7 @@ process calculate_statistics_vcf {
     pipeline_parameters += " --spring.data.mongodb.database=" + db_name.toString()
 
     """
-    java -Xmx4G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.load_job_props --parameters.path=$params.load_job_props $pipeline_parameters
+    java -Xmx${task.memory.toGiga()}G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.load_job_props --parameters.path=$params.load_job_props $pipeline_parameters
     """
 }
 
@@ -456,6 +456,6 @@ process import_accession {
     pipeline_parameters += " --spring.data.mongodb.database=" + db_name.toString()
 
     """
-    java -Xmx4G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.acc_import_job_props --parameters.path=$params.acc_import_job_props $pipeline_parameters
+    java -Xmx${task.memory.toGiga()}G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.acc_import_job_props --parameters.path=$params.acc_import_job_props $pipeline_parameters
     """
 }
diff --git a/eva_submission/nextflow/remap_and_cluster.nf b/eva_submission/nextflow/remap_and_cluster.nf
@@ -136,7 +136,7 @@ process extract_vcf_from_mongo {
     publishDir "$params.logs_dir", overwrite: true, mode: "copy", pattern: "*.log*"
 
     """
-    java -Xmx8G -jar $params.jar.vcf_extractor \
+    java -Xmx${task.memory.toGiga()}G -jar $params.jar.vcf_extractor \
         --spring.config.location=file:${params.extraction_properties} \
         --parameters.assemblyAccession=${source_assembly_accession} \
         --parameters.fasta=${source_fasta} \
@@ -200,7 +200,7 @@ process ingest_vcf_into_mongo {
 
     script:
     """
-    java -Xmx8G -jar $params.jar.vcf_ingestion \
+    java -Xmx${task.memory.toGiga()}G -jar $params.jar.vcf_ingestion \
         --spring.config.location=file:${params.ingestion_properties} \
         --parameters.remappedFrom=${source_assembly_accession} \
         --parameters.vcf=${remapped_vcf} \
@@ -226,7 +226,7 @@ process cluster_studies_from_mongo {
     publishDir "$params.logs_dir", overwrite: true, mode: "copy"
 
     """
-    java -Xmx8G -jar $params.jar.clustering \
+    java -Xmx${task.memory.toGiga()}G -jar $params.jar.clustering \
         --spring.config.location=file:${params.clustering_properties} \
         --spring.batch.job.names=STUDY_CLUSTERING_JOB \
         > ${params.target_assembly_accession}_clustering.log
@@ -248,7 +248,7 @@ process qc_clustering {
     publishDir "$params.logs_dir", overwrite: true, mode: "copy", pattern: "*.log*"
 
     """
-    java -Xmx8G -jar $params.jar.clustering \
+    java -Xmx${task.memory.toGiga()}G -jar $params.jar.clustering \
         --spring.config.location=file:${params.clustering_properties} \
         --spring.batch.job.names=NEW_CLUSTERED_VARIANTS_QC_JOB \
         > ${params.target_assembly_accession}_clustering_qc.log
@@ -272,7 +272,7 @@ process backpropagate_clusters {
     publishDir "$params.logs_dir", overwrite: true, mode: "copy", pattern: "*.log*"
 
     """
-    java -Xmx8G -jar $params.jar.clustering \
+    java -Xmx${task.memory.toGiga()}G -jar $params.jar.clustering \
         --spring.config.location=file:${params.clustering_properties} \
         --parameters.remappedFrom=${source_assembly_accession} \
         --spring.batch.job.names=BACK_PROPAGATE_NEW_RS_JOB \