Move VcfToBed to Utils.wdl.

broadinstitute · Apr 29, 2024 · 3b229a7 · 3b229a7
1 parent 0791d82
commit 3b229a7
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Showing 2 changed files with 48 additions and 45 deletions.
diff --git a/wdl/DeNovoSVsScatter.wdl b/wdl/DeNovoSVsScatter.wdl
@@ -1,6 +1,7 @@
 version 1.0
 
 import "Structs.wdl"
+import "Utils.wdl" as Utils
 
 workflow DeNovoSVsScatter {
 
@@ -27,9 +28,10 @@ workflow DeNovoSVsScatter {
 
     # Scatter genotyping over shards
     scatter (shard in vcf_files) {
-        call VcfToBed {
+        call Utils.VcfToBed as VcfToBed {
             input:
                 vcf_file=shard,
+                args="--info ALL --include-filters",
                 variant_interpretation_docker=variant_interpretation_docker,
                 runtime_attr_override = runtime_attr_vcf_to_bed
         }
@@ -156,50 +158,6 @@ task RunDeNovo {
     }
 }
 
-task VcfToBed {
-
-    input {
-        File vcf_file
-        String variant_interpretation_docker
-        RuntimeAttr? runtime_attr_override
-    }
-
-    Float vcf_size = size(vcf_file, "GB")
-
-    RuntimeAttr default_attr = object {
-        mem_gb: 3.75,
-        disk_gb: ceil(10 + vcf_size * 1.5),
-        cpu_cores: 1,
-        preemptible_tries: 2,
-        max_retries: 1,
-        boot_disk_gb: 8
-    }
-
-    RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
-
-    output {
-        File bed_output = "~{basename}.bed.gz"
-    }
-
-    String basename = basename(vcf_file, ".vcf.gz")
-    command {
-        set -exuo pipefail
-
-        svtk vcf2bed ~{vcf_file} --info ALL --include-filters ~{basename}.bed
-        bgzip ~{basename}.bed
-    }
-
-    runtime {
-        cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
-        memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GB"
-        disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
-        bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
-        preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
-        maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
-        docker: variant_interpretation_docker
-    }
-}
-
 task MergeBedFiles {
 
     input {

diff --git a/wdl/Utils.wdl b/wdl/Utils.wdl
@@ -782,3 +782,48 @@ task SubsetVcfBySamplesList {
     maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
   }
 }
+
+task VcfToBed {
+
+    input {
+        File vcf_file
+        String variant_interpretation_docker
+        String? args
+        RuntimeAttr? runtime_attr_override
+    }
+
+    Float vcf_size = size(vcf_file, "GB")
+
+    RuntimeAttr default_attr = object {
+        mem_gb: 3.75,
+        disk_gb: ceil(10 + vcf_size * 1.5),
+        cpu_cores: 1,
+        preemptible_tries: 2,
+        max_retries: 1,
+        boot_disk_gb: 8
+    }
+
+    RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
+
+    output {
+        File bed_output = "~{basename}.bed.gz"
+    }
+
+    String basename = basename(vcf_file, ".vcf.gz")
+    command {
+        set -exuo pipefail
+
+        svtk vcf2bed ~{vcf_file} --info ALL --include-filters ~{basename}.bed
+        bgzip ~{basename}.bed
+    }
+
+    runtime {
+        cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
+        memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GB"
+        disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
+        bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
+        preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
+        maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
+        docker: variant_interpretation_docker
+    }
+}