From 27c95c1ed2079bdeaaf72141ec23584e7fd05286 Mon Sep 17 00:00:00 2001
From: Yueyao Gao <gaoyueya@broadinstitute.org>
Date: Wed, 12 Jun 2024 20:57:16 -0400
Subject: [PATCH] specify bam index path

---
 CoverageProfiler/CoverageProfiler.wdl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CoverageProfiler/CoverageProfiler.wdl b/CoverageProfiler/CoverageProfiler.wdl
index 9ce6639..b99106c 100644
--- a/CoverageProfiler/CoverageProfiler.wdl
+++ b/CoverageProfiler/CoverageProfiler.wdl
@@ -58,6 +58,7 @@ workflow coverageProfile {
         gatk --java-options "-Xmx~{command_mem_mb}m" DepthOfCoverage \
             -L ~{intervals} \
             --input input/~{sampleName}.bam \
+            --read-index input/~{sampleName}.bam.bai \
             --reference ~{referenceFasta} \
             --output output/~{sampleName}