adjust GATK3 HaplotypeCaller disk size

broadinstitute · Nov 5, 2024 · c0666f8 · c0666f8
1 parent 556ff1e
commit c0666f8
Show file tree

Hide file tree

Showing 3 changed files with 10 additions and 3 deletions.
diff --git a/WholeGenomeGermlineSingleSample/pipelines/VariantCalling.wdl b/WholeGenomeGermlineSingleSample/pipelines/VariantCalling.wdl
@@ -37,6 +37,7 @@ workflow VariantCalling {
     Boolean skip_reblocking = false
     Boolean use_dragen_hard_filtering = false
     String cloud_provider
+    Int? HaplotypeCaller_disk_size_manual
   }
 
   # docker images
@@ -116,7 +117,8 @@ workflow VariantCalling {
           contamination = contamination,
           preemptible_tries = agg_preemptible_tries,
           hc_scatter = hc_divisor,
-          docker = gatk_1_3_docker
+          docker = gatk_1_3_docker,
+          HaplotypeCaller_disk_size_manual = HaplotypeCaller_disk_size_manual
       }
     }
 

diff --git a/WholeGenomeGermlineSingleSample/pipelines/WholeGenomeGermlineSingleSample.wdl b/WholeGenomeGermlineSingleSample/pipelines/WholeGenomeGermlineSingleSample.wdl
@@ -70,6 +70,7 @@ workflow WholeGenomeGermlineSingleSample {
     Boolean use_dragen_hard_filtering = false
 
     String cloud_provider
+    Int? HaplotypeCaller_disk_size_manual
   }
 
   if (dragen_functional_equivalence_mode && dragen_maximum_quality_mode) {
@@ -195,7 +196,8 @@ workflow WholeGenomeGermlineSingleSample {
       agg_preemptible_tries = papi_settings.agg_preemptible_tries,
       use_gatk3_haplotype_caller = use_gatk3_haplotype_caller_,
       use_dragen_hard_filtering = use_dragen_hard_filtering_,
-      cloud_provider = cloud_provider
+      cloud_provider = cloud_provider,
+      HaplotypeCaller_disk_size_manual = HaplotypeCaller_disk_size_manual
   }
 
   if (provide_bam_output) {

diff --git a/WholeGenomeGermlineSingleSample/tasks/GermlineVariantDiscovery.wdl b/WholeGenomeGermlineSingleSample/tasks/GermlineVariantDiscovery.wdl
@@ -29,6 +29,7 @@ task HaplotypeCaller_GATK35_GVCF {
     Int hc_scatter
     #Setting default docker value for workflows that haven't yet been azurized.
     String docker = "us.gcr.io/broad-gotc-prod/gatk:1.3.0-4.2.6.1-1649964384"
+    Int? disk_size_manual
   }
 
   parameter_meta {
@@ -38,7 +39,8 @@ task HaplotypeCaller_GATK35_GVCF {
   }
 
   Float ref_size = size(ref_fasta, "GiB") + size(ref_fasta_index, "GiB") + size(ref_dict, "GiB")
-  Int disk_size = ceil(((size(input_bam, "GiB") + 30) / hc_scatter) + ref_size) + 20
+  Int estimated_disk_size = ceil(((size(input_bam, "GiB") + 30) / hc_scatter) + ref_size) + 50
+  Int disk_size = select_first([disk_size_manual, estimated_disk_size])
 
   # We use interval_padding 500 below to make sure that the HaplotypeCaller has context on both sides around
   # the interval because the assembly uses them.
@@ -101,6 +103,7 @@ task HaplotypeCaller_GATK4_VCF {
     #Setting default docker value for workflows that haven't yet been azurized.
     String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
     Int memory_multiplier = 1
+
   }
 
   Int memory_size_mb = ceil(8000 * memory_multiplier) + 2000