Var recalmem (#35)

* increased mem for SNPsVariantRecalibrator for papiv2 * increased mem for SNPsVariantRecalibrator for papiv2 * increased memory to run on papiv2 * joint calling workflow fails on 130 genomes because SNP VariantRecalibrator runs out of memory. added optional override * removed hardset cpu * specified size type * added minimum for memory
gatk-workflows · May 7, 2019 · 2407524 · 2407524
1 parent 8618748
commit 2407524
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/joint-discovery-gatk4-fc.wdl b/joint-discovery-gatk4-fc.wdl
@@ -680,6 +680,9 @@ task SNPsVariantRecalibrator {
 
   String gatk_path
   String docker
+  Int? machine_mem_gb
+  Int auto_mem = ceil(2*size(sites_only_variant_filtered_vcf, "GB" ))
+  Int machine_mem = select_first([machine_mem_gb, if auto_mem < 7 then 7 else auto_mem])
   Int disk_size
   Int preemptible_tries
 
@@ -702,8 +705,7 @@ task SNPsVariantRecalibrator {
   }
   runtime {
     docker: docker
-    memory: "7.5 GB"
-    cpu: "2"
+    memory: machine_mem + " GB"
     disks: "local-disk " + disk_size + " HDD"
     preemptible: preemptible_tries
   }

diff --git a/joint-discovery-gatk4.wdl b/joint-discovery-gatk4.wdl
@@ -659,6 +659,9 @@ task SNPsVariantRecalibrator {
 
   String gatk_path
   String docker
+  Int? machine_mem_gb
+  Int auto_mem = ceil(2*size(sites_only_variant_filtered_vcf, "GB" ))
+  Int machine_mem = select_first([machine_mem_gb, if auto_mem < 7 then 7 else auto_mem])
   Int disk_size
   Int preemptible_tries
 
@@ -681,8 +684,7 @@ task SNPsVariantRecalibrator {
   }
   runtime {
     docker: docker
-    memory: "7.5 GB"
-    cpu: "2"
+    memory: machine_mem + " GB"
     disks: "local-disk " + disk_size + " HDD"
     preemptible: preemptible_tries
   }