From 2b062c21f3bd199b8fec00306915c26f1a77b1c4 Mon Sep 17 00:00:00 2001
From: Samuel Lee <lee.samuel.k@gmail.com>
Date: Fri, 15 Feb 2019 09:22:38 -0500
Subject: [PATCH] Exposed boot disk space for Oncotator in somatic CNV WDL.
 (#3566)

---
 scripts/cnv_wdl/somatic/cnv_somatic_oncotator_workflow.wdl | 5 ++++-
 scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl      | 2 ++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/scripts/cnv_wdl/somatic/cnv_somatic_oncotator_workflow.wdl b/scripts/cnv_wdl/somatic/cnv_somatic_oncotator_workflow.wdl
index b0098a95e0c..31bc950998f 100644
--- 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
index 1e4e98891fa..63485caaca3 100644
--- 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
         }
     }