From 19a2f85332a2ec6ae97e8dd5eddace9b3ee32f5e Mon Sep 17 00:00:00 2001
From: Ash O'Farrell <aofarrel@ucsc.edu>
Date: Thu, 22 Aug 2024 21:29:46 -0700
Subject: [PATCH] TEMPORARILY avoid using CDC varpipe reference

---
 myco_raw.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/myco_raw.wdl b/myco_raw.wdl
index 0fae20e..7a58136 100644
--- a/myco_raw.wdl
+++ b/myco_raw.wdl
@@ -20,7 +20,7 @@ workflow myco {
 		Int     clean_average_q_score          = 29
 		Boolean clean_before_decontam          = true
 		Boolean covstatsQC_skip_entirely       = false
-		Boolean decontam_use_CDC_varpipe_ref   = true
+		Boolean decontam_use_CDC_varpipe_ref   = false
 		File?   mask_bedfile
 		Int     QC_max_pct_low_coverage_sites  =    20
 		Int     QC_max_pct_unmapped            =     2