From cc1a151b0bf232377b6eeaec8ba86651c2950638 Mon Sep 17 00:00:00 2001 From: Joel Simoneau Date: Mon, 12 Feb 2024 16:01:31 -0500 Subject: [PATCH 1/2] fix: add sd_locs_vcf_index input to SDtoBAF --- wdl/BatchEvidenceMerging.wdl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/wdl/BatchEvidenceMerging.wdl b/wdl/BatchEvidenceMerging.wdl index 4225784af..fce7905fc 100644 --- a/wdl/BatchEvidenceMerging.wdl +++ b/wdl/BatchEvidenceMerging.wdl @@ -67,6 +67,7 @@ workflow BatchEvidenceMerging { input: SD_files = select_first([SD_files]), sd_locs_vcf = select_first([sd_locs_vcf]), + sd_locs_vcf_index = select_first([sd_locs_vcf]) + ".tbi", batch = batch, samples = samples, rename_samples=rename_samples, @@ -179,6 +180,7 @@ task SDtoBAF { input { Array[File] SD_files File sd_locs_vcf + File sd_locs_vcf_index String batch Array[String] samples Boolean rename_samples From 20fb698b103c68916134abeeb98c1f3fc58d1dd1 Mon Sep 17 00:00:00 2001 From: Joel Simoneau Date: Mon, 12 Feb 2024 16:04:51 -0500 Subject: [PATCH 2/2] fix: index as File --- wdl/BatchEvidenceMerging.wdl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/wdl/BatchEvidenceMerging.wdl b/wdl/BatchEvidenceMerging.wdl index fce7905fc..7dfdcceef 100644 --- a/wdl/BatchEvidenceMerging.wdl +++ b/wdl/BatchEvidenceMerging.wdl @@ -63,11 +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 = select_first([sd_locs_vcf]) + ".tbi", + sd_locs_vcf_index = sd_locs_vcf_index, batch = batch, samples = samples, rename_samples=rename_samples,