From 026a7a7222bf48e6c7b2660e18bdfdb108b0396e Mon Sep 17 00:00:00 2001
From: sridhar0605 <sridhar0605@gmail.com>
Date: Thu, 25 Jan 2024 15:17:26 -0600
Subject: [PATCH] somatic wgs

---
 definitions/somatic_wgs.wdl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/definitions/somatic_wgs.wdl b/definitions/somatic_wgs.wdl
index d68159f..7d3a7cc 100644
--- a/definitions/somatic_wgs.wdl
+++ b/definitions/somatic_wgs.wdl
@@ -177,10 +177,10 @@ workflow somaticWgs {
     reference=reference,
     reference_fai=reference_fai,
     reference_dict=reference_dict,
-    tumor_bam=tumorAlignment.final_bam,
-    tumor_bam_bai=tumorAlignment.final_bam_bai,
-    normal_bam=normalAlignment.final_bam,
-    normal_bam_bai=normalAlignment.final_bam_bai,
+    tumor_cram=tumorAlignment.final_bam,
+    tumor_cram_bai=tumorAlignment.final_bam_bai,
+    normal_cram=normalAlignment.final_bam,
+    normal_cram_bai=normalAlignment.final_bam_bai,
     roi_intervals=target_intervals,
     strelka_exome_mode=false,
     strelka_cpu_reserved=strelka_cpu_reserved,