made requested changes

broadinstitute · Jul 11, 2023 · a8810f2 · a8810f2
1 parent f64adbb
commit a8810f2
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/scripts/mitochondria_m2_wdl/AlignAndCall.wdl b/scripts/mitochondria_m2_wdl/AlignAndCall.wdl
@@ -430,15 +430,16 @@ task M2 {
    
     # runtime
     String? gatk_docker_override
-    Int mem
+    Int? mem
     Int? preemptible_tries
     Int disk_size = ceil(size(input_bam, "GB") + size(ref_fasta, "GB") + size(ref_fai, "GB")) + 20
-    Int machine_mem = if defined(mem) then mem * 1000 else 3500 # Mem is in units of GB but our command and memory runtime values are in MB
   }
 
   String output_vcf = "raw" + if compress then ".vcf.gz" else ".vcf"
   String output_vcf_index = output_vcf + if compress then ".tbi" else ".idx"
 
+  # Mem is in units of GB but our command and memory runtime values are in MB
+  Int machine_mem = if defined(mem) then mem * 1000 else 3500
   Int command_mem = machine_mem - 500
 
   meta {

diff --git a/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl b/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
@@ -253,7 +253,6 @@ task RevertSam {
     Int? preemptible_tries
     Int machine_mem = 2000
     Int disk_size = ceil(size(input_bam, "GB") * 2.5) + 20
-    Int mem = machine_mem
   }
   Int java_mem = machine_mem - 1000
 
@@ -277,7 +276,7 @@ task RevertSam {
   }
   runtime {
     disks: "local-disk " + disk_size + " HDD"
-    memory: mem + " MB"
+    memory: machine_mem + " MB"
     docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"
     preemptible: select_first([preemptible_tries, 5])
   }