diff --git a/wdl/SubsetVcfBySamples.wdl b/wdl/SubsetVcfBySamples.wdl new file mode 100644 index 000000000..0e28cce98 --- /dev/null +++ b/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 + } +} \ No newline at end of file