diff --git a/scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl b/scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl index b3c710a441f..61fd516807f 100644 --- a/scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl +++ b/scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl @@ -31,6 +31,7 @@ workflow GvsExtractCohortFromSampleNames { # set to "NONE" if all the reference data was loaded into GVS in GvsImportGenomes String drop_state = "NONE" + File? interval_list Int? extract_preemptible_override Int? extract_maxretries_override Int? extract_scatter_count_override @@ -91,6 +92,9 @@ workflow GvsExtractCohortFromSampleNames { File cohort_sample_names_file = select_first([write_array_task.output_file, cohort_sample_names]) + # allow an interval list to be passed in, but default it to our standard one if no args are here + File working_interval_list = select_first([interval_list, "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"]) + call GvsPrepareCallset.GvsPrepareCallset { input: call_set_identifier = cohort_table_prefix, @@ -130,6 +134,7 @@ workflow GvsExtractCohortFromSampleNames { split_intervals_mem_override = split_intervals_mem_override, memory_override = extract_memory_override, disk_override = extract_disk_override, + interval_list = working_interval_list, gatk_override = gatk_override, write_cost_to_db = write_cost_to_db