diff --git a/wdl/alignment.wdl b/wdl/alignment.wdl index 23888eb..bc64e89 100755 --- a/wdl/alignment.wdl +++ b/wdl/alignment.wdl @@ -170,7 +170,7 @@ workflow alignment { name=normal, ref=ref, output_dir=output_dir, - sorted_bam=bwa_tumor_control.sorted_bam, + sorted_bam=bwa_normal_control.sorted_bam, } if (umi) { @@ -179,7 +179,7 @@ workflow alignment { name=tumor, ref=ref, output_dir=output_dir, - sorted_bam=bwa_normal_control.sorted_bam, + sorted_bam=bwa_tumor_control.sorted_bam, } } @@ -189,7 +189,7 @@ workflow alignment { name=tumor, ref=ref, output_dir=output_dir, - sorted_bam=bwa_normal_control.sorted_bam, + sorted_bam=bwa_tumor_control.sorted_bam, } } }