Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)

broadinstitute · Feb 15, 2019 · 6344ad7 · 6344ad7
1 parent 1aa3c5b
commit 6344ad7
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Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/scripts/cnv_wdl/somatic/cnv_somatic_oncotator_workflow.wdl b/scripts/cnv_wdl/somatic/cnv_somatic_oncotator_workflow.wdl
@@ -11,6 +11,7 @@ workflow CNVOncotatorWorkflow {
     String? additional_args
     String? oncotator_docker
     Int? mem_gb_for_oncotator
+    Int? boot_disk_space_gb_for_oncotator
     Int? preemptible_attempts
 
     call OncotateSegments {
@@ -19,6 +20,7 @@ workflow CNVOncotatorWorkflow {
             additional_args = additional_args,
             oncotator_docker = oncotator_docker,
             mem_gb = mem_gb_for_oncotator,
+            boot_disk_space_gb = boot_disk_space_gb_for_oncotator,
             preemptible_attempts = preemptible_attempts
     }
 
@@ -36,6 +38,7 @@ task OncotateSegments {
     String? oncotator_docker
     Int? mem_gb
     Int? disk_space_gb
+    Int? boot_disk_space_gb
     Boolean use_ssd = false
     Int? cpu
     Int? preemptible_attempts
@@ -69,7 +72,7 @@ task OncotateSegments {
         disks: "local-disk " + select_first([disk_space_gb, 50]) + if use_ssd then " SSD" else " HDD"
         cpu: select_first([cpu, 1])
         preemptible: select_first([preemptible_attempts, 2])
-        bootDiskSizeGb: 50
+        bootDiskSizeGb: select_first([boot_disk_space_gb, 20])
     }
 
     output {

diff --git a/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl b/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl
@@ -131,6 +131,7 @@ workflow CNVSomaticPairWorkflow {
     String? additional_args_for_oncotator
     String? oncotator_docker
     Int? mem_gb_for_oncotator
+    Int? boot_disk_space_gb_for_oncotator
 
     Int ref_size = ceil(size(ref_fasta, "GB") + size(ref_fasta_dict, "GB") + size(ref_fasta_fai, "GB"))
     Int read_count_pon_size = ceil(size(read_count_pon, "GB"))
@@ -427,6 +428,7 @@ workflow CNVSomaticPairWorkflow {
                  additional_args = additional_args_for_oncotator,
                  oncotator_docker = oncotator_docker,
                  mem_gb_for_oncotator = mem_gb_for_oncotator,
+                 boot_disk_space_gb_for_oncotator = boot_disk_space_gb_for_oncotator,
                  preemptible_attempts = preemptible_attempts
         }
     }