fix: sambamba is not installed (#118)

stjude · Jul 18, 2023 · 366000e · 366000e
1 parent 00f181e
commit 366000e
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/dx_app/src/code.sh b/dx_app/src/code.sh
@@ -78,7 +78,7 @@ main() {
     export bam_index_path="/home/dnanexus/in/bam_index/$star_mapped_sorted_bam_prefix.bam.bai"
     export bam_index_prefix="$star_mapped_sorted_bam_prefix.bam.bai"
     mkdir -p /home/dnanexus/in/bam_index/
-    ( sambamba index $star_mapped_sorted_bam_path $bam_index_path )&
+    ( samtools index $star_mapped_sorted_bam_path $bam_index_path )&
     export bam_index_pid=$!
   fi