From fa19395b6f0c74ae03fd5e19296a61eae9d24ca0 Mon Sep 17 00:00:00 2001
From: Sage Wright <sage.wright@theiagen.com>
Date: Tue, 12 Nov 2024 17:56:00 +0000
Subject: [PATCH] fix genome_percent_coverage

---
 tasks/species_typing/mycobacterium/task_tbp_parser.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tasks/species_typing/mycobacterium/task_tbp_parser.wdl b/tasks/species_typing/mycobacterium/task_tbp_parser.wdl
index 38ca566ca..80e09baf7 100644
--- a/tasks/species_typing/mycobacterium/task_tbp_parser.wdl
+++ b/tasks/species_typing/mycobacterium/task_tbp_parser.wdl
@@ -64,7 +64,7 @@ task tbp_parser {
     echo 0.0 > AVG_DEPTH
 
     # get genome percent coverage for the entire reference genome length over min_depth
-    genome=$(samtools depth -J ~{tbprofiler_bam} | awk -F "\t" '{if ($3 >= ~{min_depth}) print;}' | wc -l )
+    genome=$(samtools depth -J ~{tbprofiler_bam} | awk -F "\t" -v min_depth=~{min_depth} '{if ($3 >= min_depth) print;}' | wc -l )
     python3 -c "print ( ($genome / 4411532 ) * 100 )" | tee GENOME_PC
 
     # get genome average depth