Readded subsetvcfbysamples

wdl/SubsetVcfBySamples.wdl

@@ -0,0 +1,35 @@
+version 1.0
+
+import "Structs.wdl"
+import "Utils.wdl" as util
+
+workflow SubsetVcfBySamples {
+  input {
+    File vcf
+    File? vcf_index
+    File list_of_samples  # List of samples to keep (default, remove_samples = false) or remove (remove_samples = true)
+    String? outfile_name
+    Boolean? remove_samples  # If false (default), keep samples in provided list. If true, remove them.
+    Boolean? remove_private_sites  # If true (default), remove sites that are private to excluded samples. If false, keep sites even if no remaining samples are non-ref.
+
+    String sv_base_mini_docker
+    RuntimeAttr? runtime_attr_subset_by_samples
+  }
+
+  call util.SubsetVcfBySamplesList {
+    input:
+      vcf = vcf,
+      vcf_idx = vcf_index,
+      list_of_samples = list_of_samples,
+      outfile_name = outfile_name,
+      remove_samples = remove_samples,
+      remove_private_sites = remove_private_sites,
+      sv_base_mini_docker = sv_base_mini_docker,
+      runtime_attr_override = runtime_attr_subset_by_samples
+  }
+
+  output {
+    File vcf_subset = SubsetVcfBySamplesList.vcf_subset
+    File vcf_subset_index = SubsetVcfBySamplesList.vcf_subset_index
+  }
+}