From 5d40844425ee436e4f938043d64ffa1cd672567b Mon Sep 17 00:00:00 2001
From: "Stephanie M. Gogarten" <sdmorris@uw.edu>
Date: Tue, 6 Aug 2024 16:52:02 -0700
Subject: [PATCH] make sure requested disk size is big enough for file

---
 extract_vcf_ids.wdl | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/extract_vcf_ids.wdl b/extract_vcf_ids.wdl
index 3f8f914..25b5ff7 100644
--- a/extract_vcf_ids.wdl
+++ b/extract_vcf_ids.wdl
@@ -31,6 +31,8 @@ task bcftools_query {
         File vcf_file
     }
 
+    Int disk_gb = ceil(size(vcf_file, "GB")*1.5) + 5
+
     command <<<
         bcftools query -f '%CHROM:%POS:%REF:%ALT\n' ~{vcf_file} > variants.txt
     >>>
@@ -41,6 +43,7 @@ task bcftools_query {
 
     runtime {
         docker: "staphb/bcftools:1.16"
+        disks: "local-disk ${disk_gb} SSD"
     }
 }