diff --git a/wdl/BatchEvidenceMerging.wdl b/wdl/BatchEvidenceMerging.wdl index 4225784af..7dfdcceef 100644 --- a/wdl/BatchEvidenceMerging.wdl +++ b/wdl/BatchEvidenceMerging.wdl @@ -63,10 +63,13 @@ workflow BatchEvidenceMerging { } } if (!defined(BAF_files)) { + File sd_locs_vcf_index = select_first([sd_locs_vcf]) + ".tbi" + call SDtoBAF { input: SD_files = select_first([SD_files]), sd_locs_vcf = select_first([sd_locs_vcf]), + sd_locs_vcf_index = sd_locs_vcf_index, batch = batch, samples = samples, rename_samples=rename_samples, @@ -179,6 +182,7 @@ task SDtoBAF { input { Array[File] SD_files File sd_locs_vcf + File sd_locs_vcf_index String batch Array[String] samples Boolean rename_samples