fix genome length calc (#166)

theiagen · Aug 8, 2022 · ec5f1a9 · ec5f1a9
1 parent 1d68d2b
commit ec5f1a9
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/tasks/quality_control/task_consensus_qc.wdl b/tasks/quality_control/task_consensus_qc.wdl
@@ -7,7 +7,7 @@ task consensus_qc {
   }
   command <<<
     if [ ~{reference_genome} ] ; then
-      GENOME_LEN=$(grep -v ">" ~{reference_genome} | wc -c)
+      GENOME_LEN=$(grep -v ">" ~{reference_genome} | tr --delete '\n' | wc -c)
     else
       # set SC2 default
       GENOME_LEN=29903