somatic wgs

wustl-oncology · Jan 25, 2024 · 026a7a7 · 026a7a7
1 parent ff3949e
commit 026a7a7
Showing 1 changed file with 4 additions and 4 deletions.
diff --git 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,