make input sequence dict validation optional

DataBiosphere · Oct 3, 2024 · 3396a60 · 3396a60
1 parent 48dcbd8
commit 3396a60
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/pipelines/imputation/scientificValidation/UpdateVcfHeaderContigs.wdl b/pipelines/imputation/scientificValidation/UpdateVcfHeaderContigs.wdl
@@ -28,6 +28,7 @@ task UpdateHeader {
         File vcf_index
         File ref_dict
         String basename
+        Boolean disable_sequence_dictionary_validation = true
 
         Int disk_size_gb = ceil(4*(size(vcf, "GiB") + size(vcf_index, "GiB"))) + 20
         String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.5.0.0"
@@ -37,6 +38,8 @@ task UpdateHeader {
     Int command_mem = memory_mb - 1500
     Int max_heap = memory_mb - 1000
 
+    String disable_sequence_dict_validation_flag = if disable_sequence_dictionary_validation then "--disable-sequence-dictionary-validation" else ""
+
     command <<<
         set -e -o pipefail
 
@@ -49,7 +52,7 @@ task UpdateHeader {
         --source-dictionary ~{ref_dict} \
         --output ~{basename}.vcf.gz \
         --replace -V input.vcf.gz \
-        --disable-sequence-dictionary-validation
+        ~{disable_sequence_dict_validation_flag}
     >>>
     runtime {
         docker: gatk_docker