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

Author: bshifaw

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
   }

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
   }